Science.gov

Sample records for advanced multi-scale modeling

  1. Advances in multi-scale modeling of solidification and casting processes

    NASA Astrophysics Data System (ADS)

    Liu, Baicheng; Xu, Qingyan; Jing, Tao; Shen, Houfa; Han, Zhiqiang

    2011-04-01

    The development of the aviation, energy and automobile industries requires an advanced integrated product/process R&D systems which could optimize the product and the process design as well. Integrated computational materials engineering (ICME) is a promising approach to fulfill this requirement and make the product and process development efficient, economic, and environmentally friendly. Advances in multi-scale modeling of solidification and casting processes, including mathematical models as well as engineering applications are presented in the paper. Dendrite morphology of magnesium and aluminum alloy of solidification process by using phase field and cellular automaton methods, mathematical models of segregation of large steel ingot, and microstructure models of unidirectionally solidified turbine blade casting are studied and discussed. In addition, some engineering case studies, including microstructure simulation of aluminum casting for automobile industry, segregation of large steel ingot for energy industry, and microstructure simulation of unidirectionally solidified turbine blade castings for aviation industry are discussed.

  2. Development of advanced materials for spallation neutron sources and radiation damage simulation based on multi-scale models

    NASA Astrophysics Data System (ADS)

    Kawai, Masayoshi; Kurishita, Hiroaki; Kokawa, Hiroyuki; Watanabe, Seiichi; Sakaguchi, Norihito; Kikuchi, Kenji; Saito, Shigeru; Yoshiie, Toshimasa; Iwase, Hiroshi; Ito, Takahiro; Hashimoto, Satoshi; Kaneko, Yoshihisa; Futakawa, Masatoshi; Ishino, Shiori; JSPS Grant Team

    2012-12-01

    This report describes the status review of the JSPS Grant Team to develop advanced materials for the spallation neutron sources and modeling of radiation damage. One of the advanced materials is a toughness enhanced, fine-grained tungsten material (W-TiC) having four-times larger fracture toughness than ordinary tungsten and appreciable RT ductility in the recrystallized state. The other is an intergranular crack (IGC)-resistant austenitic stainless steel which was processed by the grain-boundary engineering (GBE). The experimental results are devoted to corrosion in a lead-bismuth eutectic, arrest of corrosion of weld-decay, radiation damage and creep rupture as well as new technique of GBE using a laser and annealing procedure. New technique seems to be applicable to large or complicated-shaped components. A series of the multi-scale models is built up from nuclear reaction between incident particles and medium nuclei to material property change due to radiation damage. Sample calculation is made on 3 mm-thick nickel bombarded by 3 GeV protons.

  3. Multi-scale modeling in cell biology

    PubMed Central

    Meier-Schellersheim, Martin; Fraser, Iain D. C.; Klauschen, Frederick

    2009-01-01

    Biomedical research frequently involves performing experiments and developing hypotheses that link different scales of biological systems such as, for instance, the scales of intracellular molecular interactions to the scale of cellular behavior and beyond to the behavior of cell populations. Computational modeling efforts that aim at exploring such multi-scale systems quantitatively with the help of simulations have to incorporate several different simulation techniques due to the different time and space scales involved. Here, we provide a non-technical overview of how different scales of experimental research can be combined with the appropriate computational modeling techniques. We also show that current modeling software permits building and simulating multi-scale models without having to become involved with the underlying technical details of computational modeling. PMID:20448808

  4. Multi-scale modeling for sustainable chemical production.

    PubMed

    Zhuang, Kai; Bakshi, Bhavik R; Herrgård, Markus J

    2013-09-01

    With recent advances in metabolic engineering, it is now technically possible to produce a wide portfolio of existing petrochemical products from biomass feedstock. In recent years, a number of modeling approaches have been developed to support the engineering and decision-making processes associated with the development and implementation of a sustainable biochemical industry. The temporal and spatial scales of modeling approaches for sustainable chemical production vary greatly, ranging from metabolic models that aid the design of fermentative microbial strains to material and monetary flow models that explore the ecological impacts of all economic activities. Research efforts that attempt to connect the models at different scales have been limited. Here, we review a number of existing modeling approaches and their applications at the scales of metabolism, bioreactor, overall process, chemical industry, economy, and ecosystem. In addition, we propose a multi-scale approach for integrating the existing models into a cohesive framework. The major benefit of this proposed framework is that the design and decision-making at each scale can be informed, guided, and constrained by simulations and predictions at every other scale. In addition, the development of this multi-scale framework would promote cohesive collaborations across multiple traditionally disconnected modeling disciplines to achieve sustainable chemical production.

  5. Microphysics in Multi-scale Modeling System with Unified Physics

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo

    2012-01-01

    Recently, a multi-scale modeling system with unified physics was developed at NASA Goddard. It consists of (1) a cloud-resolving model (Goddard Cumulus Ensemble model, GCE model), (2) a regional scale model (a NASA unified weather research and forecast, WRF), (3) a coupled CRM and global model (Goddard Multi-scale Modeling Framework, MMF), and (4) a land modeling system. The same microphysical processes, long and short wave radiative transfer and land processes and the explicit cloud-radiation, and cloud-land surface interactive processes are applied in this multi-scale modeling system. This modeling system has been coupled with a multi-satellite simulator to use NASA high-resolution satellite data to identify the strengths and weaknesses of cloud and precipitation processes simulated by the model. In this talk, a review of developments and applications of the multi-scale modeling system will be presented. In particular, the microphysics development and its performance for the multi-scale modeling system will be presented.

  6. Multi-scale modeling of hemodynamics in the cardiovascular system

    NASA Astrophysics Data System (ADS)

    Liu, Hao; Liang, Fuyou; Wong, Jasmin; Fujiwara, Takashi; Ye, Wenjing; Tsubota, Ken-iti; Sugawara, Michiko

    2015-08-01

    The human cardiovascular system is a closed-loop and complex vascular network with multi-scaled heterogeneous hemodynamic phenomena. Here, we give a selective review of recent progress in macro-hemodynamic modeling, with a focus on geometrical multi-scale modeling of the vascular network, micro-hemodynamic modeling of microcirculation, as well as blood cellular, subcellular, endothelial biomechanics, and their interaction with arterial vessel mechanics. We describe in detail the methodology of hemodynamic modeling and its potential applications in cardiovascular research and clinical practice. In addition, we present major topics for future study: recent progress of patient-specific hemodynamic modeling in clinical applications, micro-hemodynamic modeling in capillaries and blood cells, and the importance and potential of the multi-scale hemodynamic modeling.

  7. Multi-Scale Modeling of Magnetospheric Dynamics

    NASA Technical Reports Server (NTRS)

    Kuznetsova, M. M.; Hesse, M.; Toth, G.

    2012-01-01

    Magnetic reconnection is a key element in many phenomena in space plasma, e.g. Coronal mass Ejections, Magnetosphere substorms. One of the major challenges in modeling the dynamics of large-scale systems involving magnetic reconnection is to quantifY the interaction between global evolution of the magnetosphere and microphysical kinetic processes in diffusion regions near reconnection sites. Recent advances in small-scale kinetic modeling of magnetic reconnection significantly improved our understanding of physical mechanisms controlling the dissipation in the vicinity of the reconnection site in collisionless plasma. However the progress in studies of small-scale geometries was not very helpful for large scale simulations. Global magnetosphere simulations usually include non-ideal processes in terms of numerical dissipation and/or ad hoc anomalous resistivity. Comparative studies of magnetic reconnection in small scale geometries demonstrated that MHD simulations that included non-ideal processes in terms of a resistive term 11 J did not produce fast reconnection rates observed in kinetic simulations. In collisionless magnetospheric plasma, the primary mechanism controlling the dissipation in the vicinity of the reconnection site is nongyrotropic pressure effects with spatial scales comparable with the particle Larmor radius. We utilize the global MHD code BATSRUS and replace ad hoc parameters such as "critical current density" and "anomalous resistivity" with a physically motivated model of dissipation. The primary mechanism controlling the dissipation in the vicinity of the reconnection site in incorporated into MHD description in terms of non-gyrotropic corrections to the induction equation. We will demonstrate that kinetic nongyrotropic effects can significantly alter the global magnetosphere evolution. Our approach allowed for the first time to model loading/unloading cycle in response to steady southward IMF driving. The role of solar wind parameters and

  8. Tuneable resolution as a systems biology approach for multi-scale, multi-compartment computational models.

    PubMed

    Kirschner, Denise E; Hunt, C Anthony; Marino, Simeone; Fallahi-Sichani, Mohammad; Linderman, Jennifer J

    2014-01-01

    The use of multi-scale mathematical and computational models to study complex biological processes is becoming increasingly productive. Multi-scale models span a range of spatial and/or temporal scales and can encompass multi-compartment (e.g., multi-organ) models. Modeling advances are enabling virtual experiments to explore and answer questions that are problematic to address in the wet-lab. Wet-lab experimental technologies now allow scientists to observe, measure, record, and analyze experiments focusing on different system aspects at a variety of biological scales. We need the technical ability to mirror that same flexibility in virtual experiments using multi-scale models. Here we present a new approach, tuneable resolution, which can begin providing that flexibility. Tuneable resolution involves fine- or coarse-graining existing multi-scale models at the user's discretion, allowing adjustment of the level of resolution specific to a question, an experiment, or a scale of interest. Tuneable resolution expands options for revising and validating mechanistic multi-scale models, can extend the longevity of multi-scale models, and may increase computational efficiency. The tuneable resolution approach can be applied to many model types, including differential equation, agent-based, and hybrid models. We demonstrate our tuneable resolution ideas with examples relevant to infectious disease modeling, illustrating key principles at work.

  9. Multi-scale modelling and dynamics

    NASA Astrophysics Data System (ADS)

    Müller-Plathe, Florian

    Moving from a fine-grained particle model to one of lower resolution leads, with few exceptions, to an acceleration of molecular mobility, higher diffusion coefficient, lower viscosities and more. On top of that, the level of acceleration is often different for different dynamical processes as well as for different state points. While the reasons are often understood, the fact that coarse-graining almost necessarily introduces unpredictable acceleration of the molecular dynamics severely limits its usefulness as a predictive tool. There are several attempts under way to remedy these shortcoming of coarse-grained models. On the one hand, we follow bottom-up approaches. They attempt already when the coarse-graining scheme is conceived to estimate their impact on the dynamics. This is done by excess-entropy scaling. On the other hand, we also pursue a top-down development. Here we start with a very coarse-grained model (dissipative particle dynamics) which in its native form produces qualitatively wrong polymer dynamics, as its molecules cannot entangle. This model is modified by additional temporary bonds, so-called slip springs, to repair this defect. As a result, polymer melts and solutions described by the slip-spring DPD model show correct dynamical behaviour. Read more: ``Excess entropy scaling for the segmental and global dynamics of polyethylene melts'', E. Voyiatzis, F. Müller-Plathe, and M.C. Böhm, Phys. Chem. Chem. Phys. 16, 24301-24311 (2014). [DOI: 10.1039/C4CP03559C] ``Recovering the Reptation Dynamics of Polymer Melts in Dissipative Particle Dynamics Simulations via Slip-Springs'', M. Langeloth, Y. Masubuchi, M. C. Böhm, and F. Müller-Plathe, J. Chem. Phys. 138, 104907 (2013). [DOI: 10.1063/1.4794156].

  10. Multi-Scale Modeling of Magnetospheric Reconnection

    NASA Technical Reports Server (NTRS)

    Kuznetsova, M. M.; Hesse, M.; Rastatter, L.; Toth, G.; Dezeeuw, D.; Gomobosi, T.

    2007-01-01

    One of the major challenges in modeling the magnetospheric magnetic reconnection is to quantify the interaction between large-scale global magnetospheric dynamics and microphysical processes in diffusion regions near reconnection sites. There is still considerable debate as to what degree microphysical processes on kinetic scales affect the global evolution and how important it is to substitute numerical dissipation and/or ad hoc anomalous resistivity by a physically motivated model of dissipation. Comparative studies of magnetic reconnection in small scale geometries demonstrated that MHD simulations that included non-ideal processes in terms of a resistive term $\\eta J$ did not produce the fast reconnection rates observed in kinetic simulations. For a broad range of physical parameters in collisionless magnetospheric plasma, the primary mechanism controlling the dissipation in the vicinity of the reconnection site is non-gyrotropic effects with spatial scales comparable with the particle Larmor radius. We utilize the global MHD code BATSRUS and incorporate nongyrotropic effects in diffusion regions in terms of corrections to the induction equation. We developed an algorithm to search for magnetotail reconnection sites, specifically where the magnetic field components perpendicular to the local current direction approaches zero and form an X-type configuration. Spatial scales of the diffusion region and magnitude of the reconnection electric field are calculated selfconsistently using MHD plasma and field parameters in the vicinity of the reconnection site. The location of the reconnection sites is updated during the simulations. To clarify the role of nongyrotropic effects in diffusion region on the global magnetospheric dynamic we perform simulations with steady southward IMF driving of the magnetosphere. Ideal MHD simulations with magnetic reconnection supported by numerical resistivity produce steady configuration with almost stationary near-earth neutral

  11. Blood Flow: Multi-scale Modeling and Visualization (July 2011)

    SciTech Connect

    2011-01-01

    Multi-scale modeling of arterial blood flow can shed light on the interaction between events happening at micro- and meso-scales (i.e., adhesion of red blood cells to the arterial wall, clot formation) and at macro-scales (i.e., change in flow patterns due to the clot). Coupled numerical simulations of such multi-scale flow require state-of-the-art computers and algorithms, along with techniques for multi-scale visualizations. This animation presents early results of two studies used in the development of a multi-scale visualization methodology. The fisrt illustrates a flow of healthy (red) and diseased (blue) blood cells with a Dissipative Particle Dynamics (DPD) method. Each blood cell is represented by a mesh, small spheres show a sub-set of particles representing the blood plasma, while instantaneous streamlines and slices represent the ensemble average velocity. In the second we investigate the process of thrombus (blood clot) formation, which may be responsible for the rupture of aneurysms, by concentrating on the platelet blood cells, observing as they aggregate on the wall of an aneruysm. Simulation was performed on Kraken at the National Institute for Computational Sciences. Visualization was produced using resources of the Argonne Leadership Computing Facility at Argonne National Laboratory.

  12. Blood Flow: Multi-scale Modeling and Visualization

    SciTech Connect

    2010-01-01

    Multi-scale modeling of arterial blood flow can shed light on the interaction between events happening at micro- and meso-scales (i.e., adhesion of red blood cells to the arterial wall, clot formation) and at macro-scales (i.e., change in flow patterns due to the clot). Coupled numerical simulations of such multi-scale flow require state-of-the-art computers and algorithms. Along with developing methods for multi-scale computations, techniques for multi-scale visualizations must be designed. This animation presents early results of joint efforts of teams from Brown University and Argonne National Laboratory to develop a multi-scale visualization methodology. It illustrates a flow of healthy (red) and diseased (blue) blood cells with a Dissipative Particle Dynamics (DPD) method. Each blood cell is represented by a mesh made of 500 DPD-particles, and small spheres show a sub-set of the DPD particles representing the blood plasma, while instantaneous streamlines and slices represent the ensemble average velocity. Credits: Science: Leopold Grinberg and George Karniadakis, Brown University Visualization: Joseph A. Insley and Michael E. Papka, Argonne National Laboratory This research used resources of the Argonne Leadership Computing Facility at Argonne National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under contract DE-AC02-06CH11357. This research was supported in part by the National Science Foundation through the PetaApps program and used TeraGrid resources provided by National Institute for Computational Sciences.

  13. Moist multi-scale models for the hurricane embryo

    SciTech Connect

    Majda, Andrew J.; Xing, Yulong; Mohammadian, Majid

    2010-01-01

    Determining the finite-amplitude preconditioned states in the hurricane embryo, which lead to tropical cyclogenesis, is a central issue in contemporary meteorology. In the embryo there is competition between different preconditioning mechanisms involving hydrodynamics and moist thermodynamics, which can lead to cyclogenesis. Here systematic asymptotic methods from applied mathematics are utilized to develop new simplified moist multi-scale models starting from the moist anelastic equations. Three interesting multi-scale models emerge in the analysis. The balanced mesoscale vortex (BMV) dynamics and the microscale balanced hot tower (BHT) dynamics involve simplified balanced equations without gravity waves for vertical vorticity amplification due to moist heat sources and incorporate nonlinear advective fluxes across scales. The BMV model is the central one for tropical cyclogenesis in the embryo. The moist mesoscale wave (MMW) dynamics involves simplified equations for mesoscale moisture fluctuations, as well as linear hydrostatic waves driven by heat sources from moisture and eddy flux divergences. A simplified cloud physics model for deep convection is introduced here and used to study moist axisymmetric plumes in the BHT model. A simple application in periodic geometry involving the effects of mesoscale vertical shear and moist microscale hot towers on vortex amplification is developed here to illustrate features of the coupled multi-scale models. These results illustrate the use of these models in isolating key mechanisms in the embryo in a simplified content.

  14. Science based integrated approach to advanced nuclear fuel development - integrated multi-scale multi-physics hierarchical modeling and simulation framework Part III: cladding

    SciTech Connect

    Tome, Carlos N; Caro, J A; Lebensohn, R A; Unal, Cetin; Arsenlis, A; Marian, J; Pasamehmetoglu, K

    2010-01-01

    Advancing the performance of Light Water Reactors, Advanced Nuclear Fuel Cycles, and Advanced Reactors, such as the Next Generation Nuclear Power Plants, requires enhancing our fundamental understanding of fuel and materials behavior under irradiation. The capability to accurately model the nuclear fuel systems to develop predictive tools is critical. Not only are fabrication and performance models needed to understand specific aspects of the nuclear fuel, fully coupled fuel simulation codes are required to achieve licensing of specific nuclear fuel designs for operation. The backbone of these codes, models, and simulations is a fundamental understanding and predictive capability for simulating the phase and microstructural behavior of the nuclear fuel system materials and matrices. In this paper we review the current status of the advanced modeling and simulation of nuclear reactor cladding, with emphasis on what is available and what is to be developed in each scale of the project, how we propose to pass information from one scale to the next, and what experimental information is required for benchmarking and advancing the modeling at each scale level.

  15. A Goddard Multi-Scale Modeling System with Unified Physics

    NASA Technical Reports Server (NTRS)

    Tao, W.K.; Anderson, D.; Atlas, R.; Chern, J.; Houser, P.; Hou, A.; Lang, S.; Lau, W.; Peters-Lidard, C.; Kakar, R.; Kumar, S.; Lapenta, W.; Li, X.; Matsui, T.; Rienecker, M.; Shen, B.W.; Shi, J.J.; Simpson, J.; Zeng, X.

    2008-01-01

    Numerical cloud resolving models (CRMs), which are based the non-hydrostatic equations of motion, have been extensively applied to cloud-scale and mesoscale processes during the past four decades. Recent GEWEX Cloud System Study (GCSS) model comparison projects have indicated that CRMs agree with observations in simulating various types of clouds and cloud systems from different geographic locations. Cloud resolving models now provide statistical information useful for developing more realistic physically based parameterizations for climate models and numerical weather prediction models. It is also expected that Numerical Weather Prediction (NWP) and regional scale model can be run in grid size similar to cloud resolving model through nesting technique. Current and future NASA satellite programs can provide cloud, precipitation, aerosol and other data at very fine spatial and temporal scales. It requires a coupled global circulation model (GCM) and cloud-scale model (termed a szrper-parameterization or multi-scale modeling -framework, MMF) to use these satellite data to improve the understanding of the physical processes that are responsible for the variation in global and regional climate and hydrological systems. The use of a GCM will enable global coverage, and the use of a CRM will allow for better and more sophisticated physical parameterization. NASA satellite and field campaign can provide initial conditions as well as validation through utilizing the Earth Satellite simulators. At Goddard, we have developed a multi-scale modeling system with unified physics. The modeling system consists a coupled GCM-CRM (or MMF); a state-of-the-art weather research forecast model (WRF) and a cloud-resolving model (Goddard Cumulus Ensemble model). In these models, the same microphysical schemes (2ICE, several 3ICE), radiation (including explicitly calculated cloud optical properties), and surface models are applied. In addition, a comprehensive unified Earth Satellite

  16. Multi-Scale Multi-Dimensional Ion Battery Performance Model

    2007-05-07

    The Multi-Scale Multi-Dimensional (MSMD) Lithium Ion Battery Model allows for computer prediction and engineering optimization of thermal, electrical, and electrochemical performance of lithium ion cells with realistic geometries. The model introduces separate simulation domains for different scale physics, achieving much higher computational efficiency compared to the single domain approach. It solves a one dimensional electrochemistry model in a micro sub-grid system, and captures the impacts of macro-scale battery design factors on cell performance and materialmore » usage by solving cell-level electron and heat transports in a macro grid system.« less

  17. Multi-Scale Modeling of Hypersonic Gas Flow

    NASA Astrophysics Data System (ADS)

    Boyd, Iain D.

    On March 27, 2004, NASA successfully flew the X-43A hypersonic test flight vehicle at a velocity of 5000 mph to break the aeronautics speed record that had stood for over 35 years. The final flight of the X-43A on November 16, 2004 further increased the speed record to 6,600 mph which is almost ten times the speed of sound. The very high speed attainable by hypersonic airplanes could revolutionize air travel by dramatically reducing inter-continental flight times. For example, a hypersonic flight from New York to Sydney, Australia, a distance of 10,000 miles, would take less than 2 h. Reusable hypersonic vehicles are also being researched to significantly reduce the cost of access to space. Computer modeling of the gas flows around hypersonic vehicles will play a critical part in their development. This article discusses the conditions that can prevail in certain hypersonic gas flows that require a multi-scale modeling approach.

  18. The Potential Vorticity Budget of Multi-Scale MJO Models

    NASA Astrophysics Data System (ADS)

    Back, A.; Biello, J. A.; Majda, A.

    2015-12-01

    Zhang and Ling (J. Atmos. Sci. 2012) performed a comprehensive analysis of the potential vorticity budget of the Madden-Julian Oscillation throughout its initiation and evolution. Biello and Majda have used the Intraseasonal Planetary Equatorial Synoptic-Scale Dynamics (IPESD) framework of Majda and Klein (J. Atmos. Sci. 2003) to create kinematic models of the MJO which distinguish MJO events forced by large-scale heating from MJO events forced by the upscale fluxes of momentum and temperature from the synoptic scales. In the present study, the results of Zhang and Ling provide a benchmark for comparing the different multi-scale MJO models. In particular, a potential vorticity budget can be obtained in the multiscale framework, and the advection, in-scale generation and upscale transfer of PV are considered.

  19. Multi-Scale Coupling in Ocean and Climate Modeling

    SciTech Connect

    Zhengyu Liu, Leslie Smith

    2009-08-14

    We have made significant progress on several projects aimed at understanding multi-scale dynamics in geophysical flows. Large-scale flows in the atmosphere and ocean are influenced by stable density stratification and rotation. The presence of stratification and rotation has important consequences through (i) the conservation of potential vorticity q = {omega} {center_dot} {del} {rho}, where {omega} is the total vorticity and {rho} is the density, and (ii) the existence of waves that affect the redistribution of energy from a given disturbance to the flow. Our research is centered on quantifying the effects of potential vorticity conservation and of wave interactions for the coupling of disparate time and space scales in the oceans and the atmosphere. Ultimately we expect the work to help improve predictive capabilities of atmosphere, ocean and climate modelers. The main findings of our research projects are described.

  20. A Goddard Multi-Scale Modeling System with Unified Physics

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo

    2010-01-01

    A multi-scale modeling system with unified physics has been developed at NASA Goddard Space Flight Center (GSFC). The system consists of an MMF, the coupled NASA Goddard finite-volume GCM (fvGCM) and Goddard Cumulus Ensemble model (GCE, a CRM); the state-of-the-art Weather Research and Forecasting model (WRF) and the stand alone GCE. These models can share the same microphysical schemes, radiation (including explicitly calculated cloud optical properties), and surface models that have been developed, improved and tested for different environments. In this talk, I will present: (1) A brief review on GCE model and its applications on the impact of the aerosol on deep precipitation processes, (2) The Goddard MMF and the major difference between two existing MMFs (CSU MMF and Goddard MMF), and preliminary results (the comparison with traditional GCMs), and (3) A discussion on the Goddard WRF version (its developments and applications). We are also performing the inline tracer calculation to comprehend the physical processes (i.e., boundary layer and each quadrant in the boundary layer) related to the development and structure of hurricanes and mesoscale convective systems. In addition, high - resolution (spatial. 2km, and temporal, I minute) visualization showing the model results will be presented.

  1. Multi-scale modeling of the CD8 immune response

    NASA Astrophysics Data System (ADS)

    Barbarroux, Loic; Michel, Philippe; Adimy, Mostafa; Crauste, Fabien

    2016-06-01

    During the primary CD8 T-Cell immune response to an intracellular pathogen, CD8 T-Cells undergo exponential proliferation and continuous differentiation, acquiring cytotoxic capabilities to address the infection and memorize the corresponding antigen. After cleaning the organism, the only CD8 T-Cells left are antigen-specific memory cells whose role is to respond stronger and faster in case they are presented this very same antigen again. That is how vaccines work: a small quantity of a weakened pathogen is introduced in the organism to trigger the primary response, generating corresponding memory cells in the process, giving the organism a way to defend himself in case it encounters the same pathogen again. To investigate this process, we propose a non linear, multi-scale mathematical model of the CD8 T-Cells immune response due to vaccination using a maturity structured partial differential equation. At the intracellular scale, the level of expression of key proteins is modeled by a delay differential equation system, which gives the speeds of maturation for each cell. The population of cells is modeled by a maturity structured equation whose speeds are given by the intracellular model. We focus here on building the model, as well as its asymptotic study. Finally, we display numerical simulations showing the model can reproduce the biological dynamics of the cell population for both the primary response and the secondary responses.

  2. A Goddard Multi-Scale Modeling System with Unified Physics

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo

    2010-01-01

    A multi-scale modeling system with unified physics has been developed at NASA Goddard Space Flight Center (GSFC). The system consists of an MMF, the coupled NASA Goddard finite-volume GCM (fvGCM) and Goddard Cumulus Ensemble model (GCE, a CRM); the state-of-the-art Weather Research and Forecasting model (WRF) and the stand alone GCE. These models can share the same microphysical schemes, radiation (including explicitly calculated cloud optical properties), and surface models that have been developed, improved and tested for different environments. In this talk, I will present: (1) A brief review on GCE model and its applications on the impact of the aerosol on deep precipitation processes, (2) The Goddard MMF and the major difference between two existing MMFs (CSU MMF and Goddard MMF), and preliminary results (the comparison with traditional GCMs), and (3) A discussion on the Goddard WRF version (its developments and applications). We are also performing the inline tracer calculation to comprehend the ph ysical processes (i.e., boundary layer and each quadrant in the boundary layer) related to the development and structure of hurricanes and mesoscale convective systems.

  3. Multi-Scale Modeling of Cross-Linked Nanotube Materials

    NASA Technical Reports Server (NTRS)

    Frankland, S. J. V.; Odegard, G. M.; Herzog, M. N.; Gates, T. S.; Fay, C. C.

    2005-01-01

    The effect of cross-linking single-walled carbon nanotubes on the Young's modulus of a nanotube-reinforced composite is modeled with a multi-scale method. The Young's modulus is predicted as a function of nanotube volume fraction and cross-link density. In this method, the constitutive properties of molecular representative volume elements are determined using molecular dynamics simulation and equivalent-continuum modeling. The Young's modulus is subsequently calculated for cross-linked nanotubes in a matrix which consists of the unreacted cross-linking agent. Two different cross-linking agents are used in this study, one that is short and rigid (Molecule A), and one that is long and flexible (Molecule B). Direct comparisons between the predicted elastic constants are made for the models in which the nanotubes are either covalently bonded or not chemically bonded to the cross-linking agent. At a nanotube volume fraction of 10%, the Young's modulus of Material A is not affected by nanotube crosslinking, while the Young's modulus of Material B is reduced by 64% when the nanotubes are cross-linked relative to the non-cross-linked material with the same matrix.

  4. Multi-scale Modeling of Plasticity in Tantalum.

    SciTech Connect

    Lim, Hojun; Battaile, Corbett Chandler.; Carroll, Jay; Buchheit, Thomas E.; Boyce, Brad; Weinberger, Christopher

    2015-12-01

    In this report, we present a multi-scale computational model to simulate plastic deformation of tantalum and validating experiments. In atomistic/ dislocation level, dislocation kink- pair theory is used to formulate temperature and strain rate dependent constitutive equations. The kink-pair theory is calibrated to available data from single crystal experiments to produce accurate and convenient constitutive laws. The model is then implemented into a BCC crystal plasticity finite element method (CP-FEM) model to predict temperature and strain rate dependent yield stresses of single and polycrystalline tantalum and compared with existing experimental data from the literature. Furthermore, classical continuum constitutive models describing temperature and strain rate dependent flow behaviors are fit to the yield stresses obtained from the CP-FEM polycrystal predictions. The model is then used to conduct hydro- dynamic simulations of Taylor cylinder impact test and compared with experiments. In order to validate the proposed tantalum CP-FEM model with experiments, we introduce a method for quantitative comparison of CP-FEM models with various experimental techniques. To mitigate the effects of unknown subsurface microstructure, tantalum tensile specimens with a pseudo-two-dimensional grain structure and grain sizes on the order of millimeters are used. A technique combining an electron back scatter diffraction (EBSD) and high resolution digital image correlation (HR-DIC) is used to measure the texture and sub-grain strain fields upon uniaxial tensile loading at various applied strains. Deformed specimens are also analyzed with optical profilometry measurements to obtain out-of- plane strain fields. These high resolution measurements are directly compared with large-scale CP-FEM predictions. This computational method directly links fundamental dislocation physics to plastic deformations in the grain-scale and to the engineering-scale applications. Furthermore, direct

  5. Multi-Scale Continuum Modeling of Biological Processes

    PubMed Central

    Cheng, Y; Kekenes-Huskey, P; Hake, JE; Holst, MJ; McCammon, JA; Michailova, AP

    2012-01-01

    This article provides a brief review of multi-scale modeling at the molecular to cellular scale, with new results for heart muscle cells. A finite element-based simulation package (SMOL) was used to investigate the signaling transduction at molecular and sub-cellular scales (http://mccammon.ucsd.edu/smol/, http://FETK.org) by numerical solution of time-dependent Smoluchowski equations and a reaction-diffusion system. At the molecular scale, SMOL has yielded experimentally-validated estimates of the diffusion-limited association rates for the binding of acetylcholine to mouse acetylcholinesterase using crystallographic structural data. The predicted rate constants exhibit increasingly delayed steady-state times with increasing ionic strength and demonstrate the role of an enzyme’s electrostatic potential in influencing ligand binding. At the sub-cellular scale, an extension of SMOL solves a non-linear, reaction-diffusion system describing Ca2+ ligand buffering and diffusion in experimentally-derived rodent ventricular myocyte geometries. Results reveal the important role for mobile and stationary Ca2+ buffers, including Ca2+ indicator dye. We found that the alterations in Ca2+-binding and dissociation rates of troponin C (TnC) and total TnC concentration modulate subcellular Ca2+ signals. Model predicts that reduced off-rate in whole troponin complex (TnC, TnI, TnT) versus reconstructed thin filaments (Tn, Tm, actin) alters cytosolic Ca2+ dynamics under control conditions or in disease-linked TnC mutations. The ultimate goal of these studies is to develop scalable methods and theories for integration of molecular-scale information into simulations of cellular-scale systems. PMID:23505398

  6. Carbon Capture Simulation Initiative: A Case Study in Multi-Scale Modeling and New Challenges

    SciTech Connect

    Miller, David; Syamlal, Madhava; Mebane, David; Storlie, Curtis; Bhattacharyya, Debangsu; Sahinidis, Nikolaos V.; Agarwal, Deborah A.; Tong, Charles; Zitney, Stephen E.; Sarkar, Avik; Sun, Xin; Sundaresan, Sankaran; Ryan, Emily M.; Engel, David W.; Dale, Crystal

    2014-04-01

    Advanced multi-scale modeling and simulation has the potential to dramatically reduce development time, resulting in considerable cost savings. The Carbon Capture Simulation Initiative is a partnership among national laboratories, industry and universities that is developing and deploying a suite of multi-scale modeling and simulation tools including basic data submodels, steady-state and dynamic process models, process optimization and uncertainty quantification tools, an advanced dynamic process control framework, high-resolution filtered computational-fluid-dynamic (CFD) submodels, validated high-fidelity device-scale CFD models with quantified uncertainty, and a risk analysis framework. These tools and models enable basic data submodels, including thermodynamics and kinetics, to be used within detailed process models to synthesize and optimize a process. The resulting process informs the development of process control systems and more detailed simulations of potential equipment to improve the design and reduce scale-up risk. Quantification and propagation of uncertainty across scales is an essential part of these tools and models.

  7. Carbon Capture Simulation Initiative: A Case Study in Multi-Scale Modeling and New Challenges

    SciTech Connect

    Miller, David C; Syamlal, Madhava; Zitney, Stephen E.

    2014-06-07

    Abstract: Advanced multi-scale modeling and simulation has the potential to dramatically reduce development time, resulting in considerable cost savings. The Carbon Capture Simulation Initiative is a partnership among national laboratories, industry and universities that is developing and deploying a suite of multi-scale modeling and simulation tools including basic data submodels, steady-state and dynamic process models, process optimization and uncertainty quantification tools, an advanced dynamic process control framework, high-resolution filtered computational-fluid-dynamic (CFD) submodels, validated high-fidelity device-scale CFD models with quantified uncertainty, and a risk analysis framework. These tools and models enable basic data submodels, including thermodynamics and kinetics, to be used within detailed process models to synthesize and optimize a process. The resulting process informs the development of process control systems and more detailed simulations of potential equipment to improve the design and reduce scale-up risk. Quantification and propagation of uncertainty across scales is an essential part of these tools and models.

  8. Multi-scale modelling of submarine landslide-generated tsunamis

    NASA Astrophysics Data System (ADS)

    Hill, J.; Piggott, M. D.; Collins, G. S.; Smith, R. C.; Allison, P. A.

    2013-12-01

    Submarine landslides can be far larger than terrestrial landslides and many generate destructive tsunamis. The Storegga Slide, offshore Norway, covers an area larger than Scotland and contains 3,000 km3 of material (enough to cover Scotland to a depth of 80 m). This huge slide occurred at 8.2 ka and extends for 800 km down slope. It produced a tsunami with >20 m run-up around the Norwegian Sea, including the Shetlands, and run-ups were typically 3-4 m along the mainland coast of Scotland. The tsunami propagated as far as East Greenland. Northern Europe faces few, if any, other natural hazards that could cause damage on the scale of a repeat Storegga Slide tsunami. Modelling such vast natural disasters is not straightforward. In order to achieve accurate run-up, high resolution is required near the coastlines, but entire oceans must be modelled to account for the vast distances travelled by the wave. Here, we use the open-source, three-dimensional CFD model, Fluidity, to simulate the Storegga landslide-generated tsunami. Fluidity's unstructured meshing allows resolution to vary by orders of magnitude within a single numerical simulation. We present results from multi-scale simulations that capture fine-scale coastal details and at the same time cover a domain spanning the Arctic ocean to capture run-ups on the East Greenland coast. We also compare the effects of modern vs palaeo-bathymetry, which has been neglected in previous numerical modelling studies. Future work will include assessing other potential landslide sites and how landslide dynamics affect the resulting tsunami wave to be used in hazard assessment for Northern Europe. Close-up of the computational mesh around the UK coast, western Norway and as far east as Iceland. The shift in resolution from 750m at the coast to over 20km in open water is clearly visible. Note the high resolution area to the top left which is the Storegga Landslide region.

  9. Quasi-3D Multi-scale Modeling Framework Development

    NASA Astrophysics Data System (ADS)

    Arakawa, A.; Jung, J.

    2008-12-01

    When models are truncated in or near an energetically active range of the spectrum, model physics must be changed as the resolution changes. The model physics of GCMs and that of CRMs are, however, quite different from each other and at present there is no unified formulation of model physics that automatically provides transition between these model physics. The Quasi-3D (Q3D) Multi-scale Modeling Framework (MMF) is an attempt to bridge this gap. Like the recently proposed Heterogeneous Multiscale Method (HMM) (E and Engquist 2003), MMF combines a macroscopic model, GCM, and a microscopic model, CRM. Unlike the traditional multiscale methods such as the multi-grid and adapted mesh refinement techniques, HMM and MMF are for solving multi-physics problems. They share the common objective "to design combined macroscopic-microscopic computational methods that are much more efficient than solving the full microscopic model and at the same time give the information we need" (E et al. 2008). The question is then how to meet this objective in practice, which can be highly problem dependent. In HHM, the efficiency is gained typically by localization of the microscale problem. Following the pioneering work by Grabowski and Smolarkiewicz (1999) and Grabowski (2001), MMF takes advantage of the fact that 2D CRMs are reasonably successful in simulating deep clouds. In this approach, the efficiency is gained by sacrificing the three-dimensionality of cloud-scale motion. It also "localizes" the algorithm through embedding a CRM in each GCM grid box using cyclic boundary condition. The Q3D MMF is an attempt to reduce the expense due to these constraints by partially including the cloud-scale 3D effects and extending the CRM beyond individual GCM grid boxes. As currently formulated, the Q3D MMF is a 4D estimation/prediction framework that combines a GCM with a 3D anelastic cloud-resolving vector vorticity equation model (VVM) applied to a network of horizontal grids. The network

  10. Training Systems Modelers through the Development of a Multi-scale Chagas Disease Risk Model

    NASA Astrophysics Data System (ADS)

    Hanley, J.; Stevens-Goodnight, S.; Kulkarni, S.; Bustamante, D.; Fytilis, N.; Goff, P.; Monroy, C.; Morrissey, L. A.; Orantes, L.; Stevens, L.; Dorn, P.; Lucero, D.; Rios, J.; Rizzo, D. M.

    2012-12-01

    The goal of our NSF-sponsored Division of Behavioral and Cognitive Sciences grant is to create a multidisciplinary approach to develop spatially explicit models of vector-borne disease risk using Chagas disease as our model. Chagas disease is a parasitic disease endemic to Latin America that afflicts an estimated 10 million people. The causative agent (Trypanosoma cruzi) is most commonly transmitted to humans by blood feeding triatomine insect vectors. Our objectives are: (1) advance knowledge on the multiple interacting factors affecting the transmission of Chagas disease, and (2) provide next generation genomic and spatial analysis tools applicable to the study of other vector-borne diseases worldwide. This funding is a collaborative effort between the RSENR (UVM), the School of Engineering (UVM), the Department of Biology (UVM), the Department of Biological Sciences (Loyola (New Orleans)) and the Laboratory of Applied Entomology and Parasitology (Universidad de San Carlos). Throughout this five-year study, multi-educational groups (i.e., high school, undergraduate, graduate, and postdoctoral) will be trained in systems modeling. This systems approach challenges students to incorporate environmental, social, and economic as well as technical aspects and enables modelers to simulate and visualize topics that would either be too expensive, complex or difficult to study directly (Yasar and Landau 2003). We launch this research by developing a set of multi-scale, epidemiological models of Chagas disease risk using STELLA® software v.9.1.3 (isee systems, inc., Lebanon, NH). We use this particular system dynamics software as a starting point because of its simple graphical user interface (e.g., behavior-over-time graphs, stock/flow diagrams, and causal loops). To date, high school and undergraduate students have created a set of multi-scale (i.e., homestead, village, and regional) disease models. Modeling the system at multiple spatial scales forces recognition that

  11. Multi-scale modelling of uranyl chloride solutions

    SciTech Connect

    Nguyen, Thanh-Nghi; Duvail, Magali Villard, Arnaud; Dufrêche, Jean-François; Molina, John Jairo; Guilbaud, Philippe

    2015-01-14

    Classical molecular dynamics simulations with explicit polarization have been successfully used to determine the structural and thermodynamic properties of binary aqueous solutions of uranyl chloride (UO{sub 2}Cl{sub 2}). Concentrated aqueous solutions of uranyl chloride have been studied to determine the hydration properties and the ion-ion interactions. The bond distances and the coordination number of the hydrated uranyl are in good agreement with available experimental data. Two stable positions of chloride in the second hydration shell of uranyl have been identified. The UO{sub 2}{sup 2+}-Cl{sup −} association constants have also been calculated using a multi-scale approach. First, the ion-ion potential averaged over the solvent configurations at infinite dilution (McMillan-Mayer potential) was calculated to establish the dissociation/association processes of UO{sub 2}{sup 2+}-Cl{sup −} ion pairs in aqueous solution. Then, the association constant was calculated from this potential. The value we obtained for the association constant is in good agreement with the experimental result (K{sub UO{sub 2Cl{sup +}}} = 1.48 l mol{sup −1}), but the resulting activity coefficient appears to be too low at molar concentration.

  12. Transferring Multi-Scale Approaches from 3d City Modeling to Ifc-Based Tunnel Modeling

    NASA Astrophysics Data System (ADS)

    Borrmann, A.; Kolbe, T. H.; Donaubauer, A.; Steuer, H.; Jubierre, J. R.

    2013-09-01

    A multi-scale representation of the built environment is required to provide information with the adequate level of detail (LoD) for different use cases and objectives. This applies not only to the visualization of city and building models, but in particular to their use in the context of planning and analysis tasks. While in the field of Geographic Information Systems, the handling of multi-scale representations is well established and understood, no formal approaches for incorporating multi-scale methods exist in the field of Building Information Modeling (BIM) so far. However, these concepts are much needed to better support highly dynamic planning processes that make use of very rough information about the facility under design in the early stages and provide increasingly detailed and fine-grained information in later stages. To meet these demands, this paper presents a comprehensive concept for incorporating multi-scale representations with infrastructural building information models, with a particular focus on the representation of shield tunnels. Based on a detailed analysis of the data modeling methods used in CityGML for capturing multiscale representations and the requirements present in the context of infrastructure planning projects, we discuss potential extensions to the BIM data model Industry Foundation Classes (IFC). Particular emphasis is put on providing means for preserving the consistency of the representation across the different Levels-of-Detail (LoD). To this end we make use of a procedural geometry description which makes it possible to define explicit dependencies between geometric entities on different LoDs. The modification of an object on a coarse level consequently results in an automated update of all dependent objects on the finer levels. Finally we discuss the transformation of the IFC-based multi-scale tunnel model into a CityGML compliant tunnel representation.

  13. ONE-ATMOSPHERE DYNAMICS DESCRIPTION IN THE MODELS-3 COMMUNITY MULTI-SCALE QUALITY (CMAQ) MODELING SYSTEM

    EPA Science Inventory

    This paper proposes a general procedure to link meteorological data with air quality models, such as U.S. EPA's Models-3 Community Multi-scale Air Quality (CMAQ) modeling system. CMAQ is intended to be used for studying multi-scale (urban and regional) and multi-pollutant (ozon...

  14. Multi-scale modelling of rubber-like materials and soft tissues: an appraisal

    PubMed Central

    Puglisi, G.

    2016-01-01

    We survey, in a partial way, multi-scale approaches for the modelling of rubber-like and soft tissues and compare them with classical macroscopic phenomenological models. Our aim is to show how it is possible to obtain practical mathematical models for the mechanical behaviour of these materials incorporating mesoscopic (network scale) information. Multi-scale approaches are crucial for the theoretical comprehension and prediction of the complex mechanical response of these materials. Moreover, such models are fundamental in the perspective of the design, through manipulation at the micro- and nano-scales, of new polymeric and bioinspired materials with exceptional macroscopic properties. PMID:27118927

  15. A Multi-Scale Interaction Model for Madden-Julian Oscillation

    NASA Astrophysics Data System (ADS)

    Wang, B.; Liu, F.

    2010-12-01

    Madden-Julian oscillation (MJO) is an equatorial, planetary scale circulation system coupled with a multi-scale convective complex. The nature and roles of multi-scale interaction (MSI) on MJO dynamics has not been well understood. Here we formulate a prototype theoretical model to advance our understanding the MSI in MJO. The model integrates three essential elements: a) large scale equatorial wave dynamics driven by boundary layer frictional convergence instability (FCI), b) effects of multi-cloud heating and an instability arising from synoptic system-induced convective momentum transfer (CMT), and c) interaction between the planetary and synoptic systems. We show that the CMT mechanism tends to yield a growing stationary mode with a quadrupole-vortex horizontal structure (enhanced Rossby wave component); whereas the FCI favors a fast eastward-moving mode with a Gill-Pattern structure (enhanced Kelvin wave response). The MSI instability can stem from either FCI or CMT mechanisms or both, depending on the ratio of deep convective versus stratiform/congestus heating. With increasing stratiform/congestus heating, the FCI weakens while the CMT becomes more effective. A growing MSI mode has a mixed horizontal structure of CMT and FCI and prefers slow eastward propagation. The FCI sets the eastward propagation, and CMT plays a vital role in slowing down the propagation speed. These results encourage further observational diagnosis of multi-cloud structure and heating profiles in the MJO convective complex and improvement of models’ capability in reproducing correct partitioning of cloud amounts between deep convective and stratiform/congestus clouds.

  16. Microphysics in the Multi-Scale Modeling Systems with Unified Physics

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo; Chern, J.; Lamg, S.; Matsui, T.; Shen, B.; Zeng, X.; Shi, R.

    2011-01-01

    In recent years, exponentially increasing computer power has extended Cloud Resolving Model (CRM) integrations from hours to months, the number of computational grid points from less than a thousand to close to ten million. Three-dimensional models are now more prevalent. Much attention is devoted to precipitating cloud systems where the crucial 1-km scales are resolved in horizontal domains as large as 10,000 km in two-dimensions, and 1,000 x 1,000 km2 in three-dimensions. Cloud resolving models now provide statistical information useful for developing more realistic physically based parameterizations for climate models and numerical weather prediction models. It is also expected that NWP and mesoscale model can be run in grid size similar to cloud resolving model through nesting technique. Recently, a multi-scale modeling system with unified physics was developed at NASA Goddard. It consists of (l) a cloud-resolving model (Goddard Cumulus Ensemble model, GCE model), (2) a regional scale model (a NASA unified weather research and forecast, WRF), (3) a coupled CRM and global model (Goddard Multi-scale Modeling Framework, MMF), and (4) a land modeling system. The same microphysical processes, long and short wave radiative transfer and land processes and the explicit cloud-radiation, and cloud-surface interactive processes are applied in this multi-scale modeling system. This modeling system has been coupled with a multi-satellite simulator to use NASA high-resolution satellite data to identify the strengths and weaknesses of cloud and precipitation processes simulated by the model. In this talk, the microphysics developments of the multi-scale modeling system will be presented. In particular, the results from using multi-scale modeling system to study the heavy precipitation processes will be presented.

  17. Using Multi-Scale Modeling Systems to Study the Precipitation Processes

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo

    2010-01-01

    In recent years, exponentially increasing computer power has extended Cloud Resolving Model (CRM) integrations from hours to months, the number of computational grid points from less than a thousand to close to ten million. Three-dimensional models are now more prevalent. Much attention is devoted to precipitating cloud systems where the crucial 1-km scales are resolved in horizontal domains as large as 10,000 km in two-dimensions, and 1,000 x 1,000 km2 in three-dimensions. Cloud resolving models now provide statistical information useful for developing more realistic physically based parameterizations for climate models and numerical weather prediction models. It is also expected that NWP and mesoscale model can be run in grid size similar to cloud resolving model through nesting technique. Recently, a multi-scale modeling system with unified physics was developed at NASA Goddard. It consists of (1) a cloud-resolving model (Goddard Cumulus Ensemble model, GCE model), (2) a regional scale model (a NASA unified weather research and forecast, WRF), (3) a coupled CRM and global model (Goddard Multi-scale Modeling Framework, MMF), and (4) a land modeling system. The same microphysical processes, long and short wave radiative transfer and land processes and the explicit cloud-radiation, and cloud-land surface interactive processes are applied in this multi-scale modeling system. This modeling system has been coupled with a multi-satellite simulator to use NASA high-resolution satellite data to identify the strengths and weaknesses of cloud and precipitation processes simulated by the model. In this talk, a review of developments and applications of the multi-scale modeling system will be presented. In particular, the results from using multi-scale modeling system to study the interactions between clouds, precipitation, and aerosols will be presented. Also how to use of the multi-satellite simulator to improve precipitation processes will be discussed.

  18. Using Multi-Scale Modeling Systems and Satellite Data to Study the Precipitation Processes

    NASA Technical Reports Server (NTRS)

    Tao, Wei--Kuo; Chern, J.; Lamg, S.; Matsui, T.; Shen, B.; Zeng, X.; Shi, R.

    2010-01-01

    In recent years, exponentially increasing computer power extended Cloud Resolving Model (CRM) integrations from hours to months, the number of computational grid points from less than a thousand to close to ten million. Three-dimensional models are now more prevalent. Much attention is devoted to precipitating cloud systems where the crucial 1-km scales are resolved in horizontal domains as large as 10,000 km in two-dimensions, and 1,000 x 1,000 sq km in three-dimensions. Cloud resolving models now provide statistical information useful for developing more realistic physically based parameterizations for climate models and numerical weather prediction models. It is also expected that NWP and mesoscale models can be run in grid size similar to cloud resolving models through nesting technique. Recently, a multi-scale modeling system with unified physics was developed at NASA Goddard. It consists of (1) a cloud-resolving model (Goddard Cumulus Ensemble model, GCE model). (2) a regional scale model (a NASA unified weather research and forecast, W8F). (3) a coupled CRM and global model (Goddard Multi-scale Modeling Framework, MMF), and (4) a land modeling system. The same microphysical processes, long and short wave radiative transfer and land processes and the explicit cloud-radiation and cloud-land surface interactive processes are applied in this multi-scale modeling system. This modeling system has been coupled with a multi-satellite simulator to use NASA high-resolution satellite data to identify the strengths and weaknesses of cloud and precipitation processes simulated by the model. In this talk, a review of developments and applications of the multi-scale modeling system will be presented. In particular, the results from using multi-scale modeling systems to study the interactions between clouds, precipitation, and aerosols will be presented. Also how to use the multi-satellite simulator to improve precipitation processes will be discussed.

  19. Using Multi-scale Modeling Systems to Study the Precipitation Processes

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo

    2007-01-01

    Numerical cloud models, which are based the non-hydrostatic equations of motion, have been extensively applied to cloud-scale and mesoscale processes during the past four decades. Because cloud-scale dynamics are treated explicitly, uncertainties stemming from convection that have to be parameterized in (hydrostatic) large-scale models are obviated, or at least mitigated, in cloud models. Global models will use the non-hydrostatic framework when their horizontal resolution becomes about 10 km, the theoretical limit for the hydrostatic approximation. This juncture will be reached one to two decades from now. Recently, a multi-scale modeling system with unified physics was developed at NASA Goddard. It consists of (1) a cloud-resolving model (CRM), (2) a regional scale model, (3) a coupled CRM and global model, and (4) a land modeling system. The same microphysical processes, long and short wave radiative transfer processes and the explicit cloud-radiation, and cloudland surface interactive processes are applied in this multi-scale modeling system. In this talk, a review of developments and applications of the multi-scale modeling system will be presented. In particular, the results from using multi-scale modeling system to study the interactions between clouds, precipitation, and aerosols will be presented.

  20. Multi-scale/multi-physical modeling in head/disk interface of magnetic data storage

    NASA Astrophysics Data System (ADS)

    Chung, Pil Seung; Smith, Robert; Vemuri, Sesha Hari; Jhon, Young In; Tak, Kyungjae; Moon, Il; Biegler, Lorenz T.; Jhon, Myung S.

    2012-04-01

    The model integration of the head-disk interface (HDI) in the hard disk drive system, which includes the hierarchy of highly interactive layers (magnetic layer, carbon overcoat (COC), lubricant, and air bearing system (ABS)), has recently been focused upon to resolve technical barriers and enhance reliability. Heat-assisted magnetic recording especially demands that the model simultaneously incorporates thermal and mechanical phenomena by considering the enormous combinatorial cases of materials and multi-scale/multi-physical phenomena. In this paper, we explore multi-scale/multi-physical simulation methods for HDI, which will holistically integrate magnetic layers, COC, lubricants, and ABS in non-isothermal conditions.

  1. Multi-scale finite element modeling allows the mechanics of amphibian neurulation to be elucidated

    NASA Astrophysics Data System (ADS)

    Chen, Xiaoguang; Brodland, G. Wayne

    2008-03-01

    The novel multi-scale computational approach introduced here makes possible a new means for testing hypotheses about the forces that drive specific morphogenetic movements. A 3D model based on this approach is used to investigate neurulation in the axolotl (Ambystoma mexicanum), a type of amphibian. The model is based on geometric data from 3D surface reconstructions of live embryos and from serial sections. Tissue properties are described by a system of cell-based constitutive equations, and parameters in the equations are determined from physical tests. The model includes the effects of Shroom-activated neural ridge reshaping and lamellipodium-driven convergent extension. A typical whole-embryo model consists of 10 239 elements and to run its 100 incremental time steps requires 2 days. The model shows that a normal phenotype does not result if lamellipodium forces are uniform across the width of the neural plate; but it can result if the lamellipodium forces decrease from a maximum value at the mid-sagittal plane to zero at the plate edge. Even the seemingly simple motions of neurulation are found to contain important features that would remain hidden, they were not studied using an advanced computational model. The present model operates in a setting where data are extremely sparse and an important outcome of the study is a better understanding of the role of computational models in such environments.

  2. A Multi-Scale Modeling System with Unified Physics

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo

    2008-01-01

    Numerical cloud models, which are based the non-hydrostatic equations of motion, have been extensively applied to cloud-scale and mesoscale processes during the past four decades. Because cloud-scale dynamics are treated explicitly, uncertainties stemming from convection that have to be parameterized in (hydrostatic) large-scale models are obviated, or at least mitigated, in cloud models. Global models will use the non-hydrostatic framework when their horizontal resolution becomes about 10 km, the theoretical limit for the hydrostatic approximation. This juncture will be reached one to two decades from now. In recent years, exponentially increasing computer power has extended cloud-resolving-mode1 integrations from hours to months, the number of computational grid points from less than a thousand to close to ten million. Three-dimensional models are now more prevalent. Much attention is devoted to precipitating cloud systems where the crucial 1-km scales are resolved in horizontal domains as large as 10,000 km in two-dimensions, and 1,000 x 1,000 km2 in three-dimensions. Cloud resolving models now provide statistical information useful for developing more realistic physically based parameterizations for climate models and numerical weather prediction models. It is also expected that NWP and mesoscale model can be run in grid size similar to cloud resolving model through nesting technique.

  3. Multi-scale Modeling in Clinical Oncology: Opportunities and Barriers to Success.

    PubMed

    Yankeelov, Thomas E; An, Gary; Saut, Oliver; Luebeck, E Georg; Popel, Aleksander S; Ribba, Benjamin; Vicini, Paolo; Zhou, Xiaobo; Weis, Jared A; Ye, Kaiming; Genin, Guy M

    2016-09-01

    Hierarchical processes spanning several orders of magnitude of both space and time underlie nearly all cancers. Multi-scale statistical, mathematical, and computational modeling methods are central to designing, implementing and assessing treatment strategies that account for these hierarchies. The basic science underlying these modeling efforts is maturing into a new discipline that is close to influencing and facilitating clinical successes. The purpose of this review is to capture the state-of-the-art as well as the key barriers to success for multi-scale modeling in clinical oncology. We begin with a summary of the long-envisioned promise of multi-scale modeling in clinical oncology, including the synthesis of disparate data types into models that reveal underlying mechanisms and allow for experimental testing of hypotheses. We then evaluate the mathematical techniques employed most widely and present several examples illustrating their application as well as the current gap between pre-clinical and clinical applications. We conclude with a discussion of what we view to be the key challenges and opportunities for multi-scale modeling in clinical oncology. PMID:27384942

  4. Multi-scale Modeling in Clinical Oncology: Opportunities and Barriers to Success.

    PubMed

    Yankeelov, Thomas E; An, Gary; Saut, Oliver; Luebeck, E Georg; Popel, Aleksander S; Ribba, Benjamin; Vicini, Paolo; Zhou, Xiaobo; Weis, Jared A; Ye, Kaiming; Genin, Guy M

    2016-09-01

    Hierarchical processes spanning several orders of magnitude of both space and time underlie nearly all cancers. Multi-scale statistical, mathematical, and computational modeling methods are central to designing, implementing and assessing treatment strategies that account for these hierarchies. The basic science underlying these modeling efforts is maturing into a new discipline that is close to influencing and facilitating clinical successes. The purpose of this review is to capture the state-of-the-art as well as the key barriers to success for multi-scale modeling in clinical oncology. We begin with a summary of the long-envisioned promise of multi-scale modeling in clinical oncology, including the synthesis of disparate data types into models that reveal underlying mechanisms and allow for experimental testing of hypotheses. We then evaluate the mathematical techniques employed most widely and present several examples illustrating their application as well as the current gap between pre-clinical and clinical applications. We conclude with a discussion of what we view to be the key challenges and opportunities for multi-scale modeling in clinical oncology.

  5. Modelling multi-scale deformation of amorphous glassy polymers with experimentally motivated evolution of the microstructure

    NASA Astrophysics Data System (ADS)

    Engqvist, Jonas; Wallin, Mathias; Ristinmaa, Matti; Hall, Stephen A.; Plivelic, Tomás S.

    2016-11-01

    Novel experimental data, obtained recently using advanced multi-scale experiments, have been used to develop a micro-mechanically motivated constitutive model for amorphous glassy polymers. Taking advantage of the experiments, the model makes use of a microstructural deformation gradient to incorporate the experimentally obtained deformation of the microstructure, as well as its evolving orientation. By comparing results from the model to experimental data, it is shown that the proposed approach is able to accurately predict glassy polymer deformation over a wide range of length-scales, from the macroscopic response (mm range) down to the deformation of the microstructure (nm range). The proposed model is evaluated by comparing the numerical response to experimental results on multiple scales from an inhomogeneous cold drawing experiment of glassy polycarbonate. Besides the macroscopic force-displacement response, a qualitative comparison of the deformation field at the surface of the specimen is performed. Furthermore, the predicted evolution of the fabric orientation is compared to experimental results obtained from X-ray scattering experiments. The model shows very good agreement with the experimental data over a wide range of length scales.

  6. Multi-scale gravity field modeling in space and time

    NASA Astrophysics Data System (ADS)

    Wang, Shuo; Panet, Isabelle; Ramillien, Guillaume; Guilloux, Frédéric

    2016-04-01

    The Earth constantly deforms as it undergoes dynamic phenomena, such as earthquakes, post-glacial rebound and water displacement in its fluid envelopes. These processes have different spatial and temporal scales and are accompanied by mass displacements, which create temporal variations of the gravity field. Since 2002, the GRACE satellite missions provide an unprecedented view of the gravity field spatial and temporal variations. Gravity models built from these satellite data are essential to study the Earth's dynamic processes (Tapley et al., 2004). Up to present, time variations of the gravity field are often modelled using spatial spherical harmonics functions averaged over a fixed period, as 10 days or 1 month. This approach is well suited for modeling global phenomena. To better estimate gravity related to local and/or transient processes, such as earthquakes or floods, and adapt the temporal resolution of the model to its spatial resolution, we propose to model the gravity field using localized functions in space and time. For that, we build a model of the gravity field in space and time with a four-dimensional wavelet basis, well localized in space and time. First we design the 4D basis, then, we study the inverse problem to model the gravity field from the potential differences between the twin GRACE satellites, and its regularization using prior knowledge on the water cycle. Our demonstration of surface water mass signals decomposition in time and space is based on the use of synthetic along-track gravitational potential data. We test the developed approach on one year of 4D gravity modeling and compare the reconstructed water heights to those of the input hydrological model. Perspectives of this work is to apply the approach on real GRACE data, addressing the challenge of a realistic noise, to better describe and understand physical processus with high temporal resolution/low spatial resolution or the contrary.

  7. Multi-Scale Distributed Sensitivity Analysis of Radiative Transfer Model

    NASA Astrophysics Data System (ADS)

    Neelam, M.; Mohanty, B.

    2015-12-01

    Amidst nature's great variability and complexity and Soil Moisture Active Passive (SMAP) mission aims to provide high resolution soil moisture products for earth sciences applications. One of the biggest challenges still faced by the remote sensing community are the uncertainties, heterogeneities and scaling exhibited by soil, land cover, topography, precipitation etc. At each spatial scale, there are different levels of uncertainties and heterogeneities. Also, each land surface variable derived from various satellite mission comes with their own error margins. As such, soil moisture retrieval accuracy is affected as radiative model sensitivity changes with space, time, and scale. In this paper, we explore the distributed sensitivity analysis of radiative model under different hydro-climates and spatial scales, 1.5 km, 3 km, 9km and 39km. This analysis is conducted in three different regions Iowa, U.S.A (SMEX02), Arizona, USA (SMEX04) and Winnipeg, Canada (SMAPVEX12). Distributed variables such as soil moisture, soil texture, vegetation and temperature are assumed to be uncertain and are conditionally simulated to obtain uncertain maps, whereas roughness data which is spatially limited are assumed a probability distribution. The relative contribution of the uncertain model inputs to the aggregated model output is also studied, using various aggregation techniques. We use global sensitivity analysis (GSA) to conduct this analysis across spatio-temporal scales. Keywords: Soil moisture, radiative transfer, remote sensing, sensitivity, SMEX02, SMAPVEX12.

  8. Multi-Scale Modeling of Global of Magnetospheric Dynamics

    NASA Technical Reports Server (NTRS)

    Kuznetsova, M. M.; Hesse, M.; Rastatter, L.; Toth, G.; DeZeeuw, D.; Gombosi, T.

    2010-01-01

    To understand the role of magnetic reconnection in global evolution of magnetosphere and to place spacecraft observations into global context it is essential to perform global simulations with physically motivated model of dissipation that is capable to reproduce reconnection rates predicted by kinetic models. In our efforts to bridge the gap between small scale kinetic modeling and global simulations we introduced an approach that allows to quantify the interaction between large-scale global magnetospheric dynamics and microphysical processes in diffusion regions near reconnection sites. We utilized the high resolution global MHD code BATSRUS and incorporate primary mechanism controlling the dissipation in the vicinity of reconnection sites in terms of kinetic corrections to induction and energy equations. One of the key elements of the multiscale modeling of magnetic reconnection is identification of reconnection sites and boundaries of surrounding diffusion regions where non-MHD corrections are required. Reconnection site search in the equatorial plane implemented in our previous studies is extended to cusp and magnetopause reconnection, as well as for magnetotail reconnection in realistic asymmetric configurations. The role of feedback between the non-ideal effects in diffusion regions and global magnetosphere structure and dynamics will be discussed.

  9. Multi-scale modeling and synthesis of polyester ionomers.

    PubMed

    Nikolić, Dragan; Moffat, Karen A; Farrugia, Valerie M; Kobryn, Alexander E; Gusarov, Sergey; Wosnick, Jordan H; Kovalenko, Andriy

    2013-04-28

    Simulations of microphase separation are carried out using the dissipative particle dynamics (DPD). By varying the concentration and temperature of resin solutions we explore mesomorphologies supported by the all-atom models. We found that for a low degree of functionalization the homogeneously distributed ionomers self-assemble into spherical micelles at solid loads below 31 wt%, subject to the activation energy barrier for the gradual growth of pre-micellar aggregates. Computed optimum aggregation numbers exhibit sensitivity to both the temperature-dependent interfacial tension and the ionic content and compare well with the experimental observations. PMID:23507929

  10. Multi-scale modelling for HEDP experiments on Orion

    NASA Astrophysics Data System (ADS)

    Sircombe, N. J.; Ramsay, M. G.; Hughes, S. J.; Hoarty, D. J.

    2016-05-01

    The Orion laser at AWE couples high energy long-pulse lasers with high intensity short-pulses, allowing material to be compressed beyond solid density and heated isochorically. This experimental capability has been demonstrated as a platform for conducting High Energy Density Physics material properties experiments. A clear understanding of the physics in experiments at this scale, combined with a robust, flexible and predictive modelling capability, is an important step towards more complex experimental platforms and ICF schemes which rely on high power lasers to achieve ignition. These experiments present a significant modelling challenge, the system is characterised by hydrodynamic effects over nanoseconds, driven by long-pulse lasers or the pre-pulse of the petawatt beams, and fast electron generation, transport, and heating effects over picoseconds, driven by short-pulse high intensity lasers. We describe the approach taken at AWE; to integrate a number of codes which capture the detailed physics for each spatial and temporal scale. Simulations of the heating of buried aluminium microdot targets are discussed and we consider the role such tools can play in understanding the impact of changes to the laser parameters, such as frequency and pre-pulse, as well as understanding effects which are difficult to observe experimentally.

  11. A top-down multi-scale modeling for actuation response of polymeric artificial muscles

    NASA Astrophysics Data System (ADS)

    Yang, Qianxi; Li, Guoqiang

    2016-07-01

    A class of innovative artificial muscles made of high-strength polymeric fibers such as fishing lines or sewing threads have been discovered recently. These muscles are fabricated by a simple "twist-insertion" procedure, which have attracted increasing attention due to their low cost and readily availability, giant tensile stroke, record energy density, and easy controllability. In the present paper, we established a multi-scale modeling framework for the thermomechanical actuation responses by a top-down strategy, spanning from macro-scale helical spring analysis down to molecular level chain interaction study. Comparison between modeling results and experimental results exhibited excellent agreement. The effect of the micro-, meso- and macro-scale parameters on the actuation responses of the artificial muscle was further discussed through a parametric study per the validated model. This work helps understand the physical origin behind the remarkable tensile actuation behavior of the twisted-then-coiled polymeric artificial muscles and also provides inspirations for optimal design of advanced artificial muscles made by twist-insertion procedure.

  12. SLIM: A multi-scale model of the land-sea continuum

    NASA Astrophysics Data System (ADS)

    De Maet, T.; Hanert, E.; Deleersnijder, E.; Fichefet, T.; Legat, V.; Remacle, J. F.; Soares Frazao, S.; Vanclooster, M.; Lambrechts, J.; König Beatty, C.; Bouillon, S.; de Brye, B.; Gourgue, O.; Kärnä, T.; Lietaer, O.; Pestiaux, A.; Slaoui, K.; Thomas, C.

    2012-04-01

    The hydrosphere is made up of a number media, such as the oceans, the shelf seas, the estuaries, the rivers, the land surface and ground water as well as the sea ice - which, for the sake of simplicity, is considered herein to be part of the hydrosphere. The processes taking place in these domains are vastly different in nature and are characterized by a wide range of space- and time-scales. The components of the hydrosphere interact with each other. For instance, the shallow marine and estuarine regions, though accounting for less than 1% of the volume of the oceans, have a biomass far from negligible as compared to that of the oceans, implying that they play a significant role in global biogeochemical cycles. This is one of the reasons why models are now needed that deal with most, if not all, of the components of the hydrospheric system. Numerical models of each of the components of the hydrosphere already exist. However, an integrated model of the whole hydrosphere has yet to be developed. Building such a model is a daunting task, requiring the development of multi-scale/physics simulation tools. Numerical methods for dealing with multi-scale problems are developing rapidly. Unstructured meshes offer an almost infinite geometrical flexibility, allowing the space resolution to be increased when and where necessary. In addition, time steppings for dealing with a wide spectrum of timescales while retaining a high order of accuracy have been developed over recent years (e.g. multi-rate schemes). The Discontinuous Galerkin Finite Element (DGFE) framework SLIM is at his third implementation. It has been build on the GMSH code (http://geuz.org/gmsh), which a state-of-the-art open-source meshing tool. This allows the use of the same definitions and easy interactions between the mesher and the model. Moreover, this provides the same user interface for meshing and visualizing results. It also enables the use of the most recent advances in mesh generation, as GMSH has a

  13. Multi-class and multi-scale models of complex biological phenomena.

    PubMed

    Yu, Jessica S; Bagheri, Neda

    2016-06-01

    Computational modeling has significantly impacted our ability to analyze vast (and exponentially increasing) quantities of experimental data for a variety of applications, such as drug discovery and disease forecasting. Single-scale, single-class models persist as the most common group of models, but biological complexity often demands more sophisticated approaches. This review surveys modeling approaches that are multi-class (incorporating multiple model types) and/or multi-scale (accounting for multiple spatial or temporal scales) and describes how these models, and combinations thereof, should be used within the context of the problem statement. We end by highlighting agent-based models as an intuitive, modular, and flexible framework within which multi-scale and multi-class models can be implemented. PMID:27115496

  14. Using Multi-Scale Modeling Systems and Satellite Data to Study the Precipitation Processes

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo; Chern, J.; Lamg, S.; Matsui, T.; Shen, B.; Zeng, X.; Shi, R.

    2011-01-01

    In recent years, exponentially increasing computer power has extended Cloud Resolving Model (CRM) integrations from hours to months, the number of computational grid points from less than a thousand to close to ten million. Three-dimensional models are now more prevalent. Much attention is devoted to precipitating cloud systems where the crucial 1-km scales are resolved in horizontal domains as large as 10,000 km in two-dimensions, and 1,000 x 1,000 km2 in three-dimensions. Cloud resolving models now provide statistical information useful for developing more realistic physically based parameterizations for climate models and numerical weather prediction models. It is also expected that NWP and mesoscale model can be run in grid size similar to cloud resolving model through nesting technique. Recently, a multi-scale modeling system with unified physics was developed at NASA Goddard. It consists of (l) a cloud-resolving model (Goddard Cumulus Ensemble model, GCE model), (2) a regional scale model (a NASA unified weather research and forecast, WRF), (3) a coupled CRM and global model (Goddard Multi-scale Modeling Framework, MMF), and (4) a land modeling system. The same microphysical processes, long and short wave radiative transfer and land processes and the explicit cloud-radiation, and cloud-land surface interactive processes are applied in this multi-scale modeling system. This modeling system has been coupled with a multi-satellite simulator to use NASA high-resolution satellite data to identify the strengths and weaknesses of cloud and precipitation processes simulated by the model. In this talk, the recent developments and applications of the multi-scale modeling system will be presented. In particular, the results from using multi-scale modeling system to study the precipitating systems and hurricanes/typhoons will be presented. The high-resolution spatial and temporal visualization will be utilized to show the evolution of precipitation processes. Also how to

  15. Voluntary EMG-to-force estimation with a multi-scale physiological muscle model

    PubMed Central

    2013-01-01

    Background EMG-to-force estimation based on muscle models, for voluntary contraction has many applications in human motion analysis. The so-called Hill model is recognized as a standard model for this practical use. However, it is a phenomenological model whereby muscle activation, force-length and force-velocity properties are considered independently. Perreault reported Hill modeling errors were large for different firing frequencies, level of activation and speed of contraction. It may be due to the lack of coupling between activation and force-velocity properties. In this paper, we discuss EMG-force estimation with a multi-scale physiology based model, which has a link to underlying crossbridge dynamics. Differently from the Hill model, the proposed method provides dual dynamics of recruitment and calcium activation. Methods The ankle torque was measured for the plantar flexion along with EMG measurements of the medial gastrocnemius (GAS) and soleus (SOL). In addition to Hill representation of the passive elements, three models of the contractile parts have been compared. Using common EMG signals during isometric contraction in four able-bodied subjects, torque was estimated by the linear Hill model, the nonlinear Hill model and the multi-scale physiological model that refers to Huxley theory. The comparison was made in normalized scale versus the case in maximum voluntary contraction. Results The estimation results obtained with the multi-scale model showed the best performances both in fast-short and slow-long term contraction in randomized tests for all the four subjects. The RMS errors were improved with the nonlinear Hill model compared to linear Hill, however it showed limitations to account for the different speed of contractions. Average error was 16.9% with the linear Hill model, 9.3% with the modified Hill model. In contrast, the error in the multi-scale model was 6.1% while maintaining a uniform estimation performance in both fast and slow

  16. A multi-scale urban atmospheric dispersion model for emergency management

    NASA Astrophysics Data System (ADS)

    Miao, Yucong; Liu, Shuhua; Zheng, Hui; Zheng, Yijia; Chen, Bicheng; Wang, Shu

    2014-11-01

    To assist emergency management planning and prevention in case of hazardous chemical release into the atmosphere, especially in densely built-up regions with large populations, a multi-scale urban atmospheric dispersion model was established. Three numerical dispersion experiments, at horizontal resolutions of 10 m, 50 m and 3000 m, were performed to estimate the adverse effects of toxic chemical release in densely built-up areas. The multi-scale atmospheric dispersion model is composed of the Weather Forecasting and Research (WRF) model, the Open Source Field Operation and Manipulation software package, and a Lagrangian dispersion model. Quantification of the adverse health effects of these chemical release events are given by referring to the U.S. Environmental Protection Agency's Acute Exposure Guideline Levels. The wind fields of the urban-scale case, with 3 km horizontal resolution, were simulated by the Beijing Rapid Update Cycle system, which were utilized by the WRF model. The sub-domain-scale cases took advantage of the computational fluid dynamics method to explicitly consider the effects of buildings. It was found that the multi-scale atmospheric dispersion model is capable of simulating the flow pattern and concentration distribution on different scales, ranging from several meters to kilometers, and can therefore be used to improve the planning of prevention and response programs.

  17. Modelling neural informational propagation and functional auditory sensory memory with temporal multi-scale operators.

    PubMed

    Serman, Maja; Serman, Nikola; Griffith, Niall J L

    2007-08-01

    In this paper we prove that both diffusion and the leaky integrators cascade based transport mechanisms have as their inherent property the effect of temporal multi-scaling. The two transport mechanisms are modeled not as convolution based algorithms but as causal physical processes. This implies that propagation of information through a neural map may act as a mechanism for achieving temporal multi-scale analysis in the auditory system. Specifically, we are interested in the effects of such a transport process on the formation and the dynamics of auditory sensory memory. Two temporal models of information propagation are discussed and compared in terms of their ability to model auditory sensory memory effects and the biological plausibility of their structure: the causal diffusion based operator (CD) and the leaky integrator cascade based operator (LINC). We show that temporal multi-scale representations achieved by both models exhibit the effects similar to those of auditory sensory memory (filtering, time delay and binding of information). As regards higher-level functions of auditory sensory memory such as change detection, the LINC operator seems to be a biologically more plausible solution for modeling temporal cortical processing.

  18. Multi-Scale Modeling of a Graphite-Epoxy-Nanotube System

    NASA Technical Reports Server (NTRS)

    Frankland, S. J. V.; Riddick, J. C.; Gates, T. S.

    2005-01-01

    A multi-scale method is utilized to determine some of the constitutive properties of a three component graphite-epoxy-nanotube system. This system is of interest because carbon nanotubes have been proposed as stiffening and toughening agents in the interlaminar regions of carbon fiber/epoxy laminates. The multi-scale method uses molecular dynamics simulation and equivalent-continuum modeling to compute three of the elastic constants of the graphite-epoxy-nanotube system: C11, C22, and C33. The 1-direction is along the nanotube axis, and the graphene sheets lie in the 1-2 plane. It was found that the C11 is only 4% larger than the C22. The nanotube therefore does have a small, but positive effect on the constitutive properties in the interlaminar region.

  19. Evaluating and Improving Cloud Processes in the Multi-Scale Modeling Framework

    SciTech Connect

    Ackerman, Thomas P.

    2015-03-01

    The research performed under this grant was intended to improve the embedded cloud model in the Multi-scale Modeling Framework (MMF) for convective clouds by using a 2-moment microphysics scheme rather than the single moment scheme used in all the MMF runs to date. The technical report and associated documents describe the results of testing the cloud resolving model with fixed boundary conditions and evaluation of model results with data. The overarching conclusion is that such model evaluations are problematic because errors in the forcing fields control the results so strongly that variations in parameterization values cannot be usefully constrained

  20. Continuum Level Formulation and Implementation of a Multi-scale Model for Vanadium

    SciTech Connect

    Lawrence Livermore National Laboratory

    2009-08-17

    A multi-scale approach is used to construct a continuum strength model for vanadium. The model is formulated assuming plastic deformation by dislocation motion and strain hardening due to dislocation interactions. Dislocation density is adopted as the state variable in the model. Information from molecular statics, molecular dynamics and dislocation dynamics simulations is combined to create kinetic relations for dislocation motion, strain hardening relations and evolution equations for the dislocation density. Implicit time integration of the constitutive equations is described in the context of implementation in a finite element code. Results are provided illustrating the strain, strain rate, temperature and pressure dependence of the constitutive model.

  1. Multi-scale groundwater modelling for the assessment of sustainable borehole yields under drought

    NASA Astrophysics Data System (ADS)

    Upton, Kirsty; Butler, Adrian; Jackson, Chris; Jones, Mike

    2014-05-01

    A new multi-scale groundwater modelling methodology is presented for simulating abstraction boreholes in regional groundwater models. This provides a robust tool for assessing the sustainable yield of supply boreholes, thus improving our understanding of groundwater availability during droughts. The yield of an abstraction well is dependent on a number of factors. These include antecedent recharge and groundwater conditions; the properties of a regional aquifer system; requirements on a groundwater system to maintain river flows or sites of ecological significance; the properties of an individual abstraction borehole; small-scale aquifer heterogeneity around a borehole; the rate of abstraction; and the way in which neighboring abstraction boreholes interact. These factors can all be represented in the multi-scale model, which couples a small-scale radial flow model of an abstraction borehole with a regional-scale groundwater model. The regional groundwater model, ZOOMQ3D, represents the large-scale groundwater system, including lateral and vertical aquifer heterogeneity, rivers, and spatially varying recharge. The 3D radial flow model, SPIDERR, represents linear and non-linear flow to a borehole, local vertical heterogeneity, well storage and pump location. The multi-scale model is applied to a supply borehole (operated by Thames Water) located in the Chalk aquifer within the catchment of the River Thames in southern England. Groundwater abstraction from the Chalk aquifer accounts for 40-70% of the total public water supply in this region. Drought is a recurring feature of the UK climate, and in particular the south and east of England. Since 1850, nine major groundwater droughts have occurred, all of which lasted longer than one year. The most recent occurred in 2010-2012, during which seven water supply companies introduced water usage restrictions, affecting over 20 million people. The radial flow model is initially calibrated against pumping test data from the

  2. Aerosol effects on deep convection in a multi-scale aerosol-climate model

    NASA Astrophysics Data System (ADS)

    Wang, M.; Ghan, S. J.; Morrison, H.

    2012-12-01

    Aerosols have been demonstrated to affect convective clouds and precipitation in observations, process models, and regional climate models. However, examining aerosol effects on convective clouds and precipitation in global climate models has been extremely challenging, as until recently the treatments in the few global climate models that include aerosol effects on convective clouds have used conventional cumulus parameterizations and hence have been quite crude. We have recently built a multi-scale aerosol-climate model, PNNL-MMF, which is an extension of a multi-scale modeling framework (MMF) model. The extended model explicitly treats aerosol effects on deep convection using a two-moment cloud microphysics scheme in the cloud-resolving model component of the MMF. In this presentation, we examine aerosol effects on convective clouds at the global scale using the PNNL-MMF model. Our results show that the frequency of precipitation occurrence at a given liquid water path increases with increasing aerosol loading for deep clouds with surface precipitation rate larger than 10 mm/day. This relationship is particularly evident during the summer time, when convection activity is strong, and may indicate invigoration of deep convection by aerosols. The modeled relationship of aerosols, clouds and precipitation is further compared with observations from the ARM long-term sites (e.g., SGP). The causes of the modeled relationship of aerosols, clouds and precipitations are examined by using a pair of 5-year MMF simulations with and without anthropogenic aerosols.

  3. Integration of multi-scale biosimulation models via light-weight semantics.

    PubMed

    Gennari, John H; Neal, Maxwell L; Carlson, Brian E; Cook, Daniel L

    2008-01-01

    Currently, biosimulation researchers use a variety of computational environments and languages to model biological processes. Ideally, researchers should be able to semiautomatically merge models to more effectively build larger, multi-scale models. However, current modeling methods do not capture the underlying semantics of these models sufficiently to support this type of model construction. In this paper, we both propose a general approach to solve this problem, and we provide a specific example that demonstrates the benefits of our methodology. In particular, we describe three biosimulation models: (1) a cardio-vascular fluid dynamics model, (2) a model of heart rate regulation via baroreceptor control, and (3) a sub-cellular-level model of the arteriolar smooth muscle. Within a light-weight ontological framework, we leverage reference ontologies to match concepts across models. The light-weight ontology then helps us combine our three models into a merged model that can answer questions beyond the scope of any single model.

  4. A multi-scale model for correlation in B cell VDJ usage of zebrafish

    NASA Astrophysics Data System (ADS)

    Pan, Keyao; Deem, Michael W.

    2011-10-01

    The zebrafish (Danio rerio) is one of the model animals used for the study of immunology because the dynamics in the adaptive immune system of zebrafish are similar to that in higher animals. In this work, we built a multi-scale model to simulate the dynamics of B cells in the primary and secondary immune responses of zebrafish. We use this model to explain the reported correlation between VDJ usage of B cell repertoires in individual zebrafish. We use a delay ordinary differential equation (ODE) system to model the immune responses in the 6-month lifespan of a zebrafish. This mean field theory gives the number of high-affinity B cells as a function of time during an infection. The sequences of those B cells are then taken from a distribution calculated by a 'microscopic' random energy model. This generalized NK model shows that mature B cells specific to one antigen largely possess a single VDJ recombination. The model allows first-principle calculation of the probability, p, that two zebrafish responding to the same antigen will select the same VDJ recombination. This probability p increases with the B cell population size and the B cell selection intensity. The probability p decreases with the B cell hypermutation rate. The multi-scale model predicts correlations in the immune system of the zebrafish that are highly similar to that from experiment.

  5. Improved convergence of gradient-based reconstruction using multi-scale models

    SciTech Connect

    Cunningham, G.S.; Hanson, K.M.; Koyfman, I.

    1996-05-01

    Geometric models have received increasing attention in medical imaging for tasks such as segmentation, reconstruction, restoration, and registration. In order to determine the best configuration of the geometric model in the context of any of these tasks, one needs to perform a difficult global optimization of an energy function that may have many local minima. Explicit models of geometry, also called deformable models, snakes, or active contours, have been used extensively to solve image segmentation problems in a non-Bayesian framework. Researchers have seen empirically that multi-scale analysis is useful for convergence to a configuration that is near the global minimum. In this type of analysis, the image data are convolved with blur functions of increasing resolution, and an optimal configuration of the snake is found for each blurred image. The configuration obtained using the highest resolution blur is used as the solution to the global optimization problem. In this article, the authors use explicit models of geometry for a variety of Bayesian estimation problems, including image segmentation, reconstruction and restoration. The authors introduce a multi-scale approach that blurs the geometric model, rather than the image data, and show that this approach turns a global, highly nonquadratic optimization into a sequence of local, approximately quadratic problems that converge to the global minimum. The result is a deterministic, robust, and efficient optimization strategy applicable to a wide variety of Bayesian estimation problems in which geometric models of images are an important component.

  6. Multi-scale Modeling of the Cardiovascular System: Disease Development, Progression, and Clinical Intervention.

    PubMed

    Zhang, Yanhang; Barocas, Victor H; Berceli, Scott A; Clancy, Colleen E; Eckmann, David M; Garbey, Marc; Kassab, Ghassan S; Lochner, Donna R; McCulloch, Andrew D; Tran-Son-Tay, Roger; Trayanova, Natalia A

    2016-09-01

    Cardiovascular diseases (CVDs) are the leading cause of death in the western world. With the current development of clinical diagnostics to more accurately measure the extent and specifics of CVDs, a laudable goal is a better understanding of the structure-function relation in the cardiovascular system. Much of this fundamental understanding comes from the development and study of models that integrate biology, medicine, imaging, and biomechanics. Information from these models provides guidance for developing diagnostics, and implementation of these diagnostics to the clinical setting, in turn, provides data for refining the models. In this review, we introduce multi-scale and multi-physical models for understanding disease development, progression, and designing clinical interventions. We begin with multi-scale models of cardiac electrophysiology and mechanics for diagnosis, clinical decision support, personalized and precision medicine in cardiology with examples in arrhythmia and heart failure. We then introduce computational models of vasculature mechanics and associated mechanical forces for understanding vascular disease progression, designing clinical interventions, and elucidating mechanisms that underlie diverse vascular conditions. We conclude with a discussion of barriers that must be overcome to provide enhanced insights, predictions, and decisions in pre-clinical and clinical applications.

  7. Multi-Scale Computational Modeling of Two-Phased Metal Using GMC Method

    NASA Technical Reports Server (NTRS)

    Moghaddam, Masoud Ghorbani; Achuthan, A.; Bednacyk, B. A.; Arnold, S. M.; Pineda, E. J.

    2014-01-01

    A multi-scale computational model for determining plastic behavior in two-phased CMSX-4 Ni-based superalloys is developed on a finite element analysis (FEA) framework employing crystal plasticity constitutive model that can capture the microstructural scale stress field. The generalized method of cells (GMC) micromechanics model is used for homogenizing the local field quantities. At first, GMC as stand-alone is validated by analyzing a repeating unit cell (RUC) as a two-phased sample with 72.9% volume fraction of gamma'-precipitate in the gamma-matrix phase and comparing the results with those predicted by finite element analysis (FEA) models incorporating the same crystal plasticity constitutive model. The global stress-strain behavior and the local field quantity distributions predicted by GMC demonstrated good agreement with FEA. High computational saving, at the expense of some accuracy in the components of local tensor field quantities, was obtained with GMC. Finally, the capability of the developed multi-scale model linking FEA and GMC to solve real life sized structures is demonstrated by analyzing an engine disc component and determining the microstructural scale details of the field quantities.

  8. Modelling future impacts of air pollution using the multi-scale UK Integrated Assessment Model (UKIAM).

    PubMed

    Oxley, Tim; Dore, Anthony J; ApSimon, Helen; Hall, Jane; Kryza, Maciej

    2013-11-01

    Integrated assessment modelling has evolved to support policy development in relation to air pollutants and greenhouse gases by providing integrated simulation tools able to produce quick and realistic representations of emission scenarios and their environmental impacts without the need to re-run complex atmospheric dispersion models. The UK Integrated Assessment Model (UKIAM) has been developed to investigate strategies for reducing UK emissions by bringing together information on projected UK emissions of SO2, NOx, NH3, PM10 and PM2.5, atmospheric dispersion, criteria for protection of ecosystems, urban air quality and human health, and data on potential abatement measures to reduce emissions, which may subsequently be linked to associated analyses of costs and benefits. We describe the multi-scale model structure ranging from continental to roadside, UK emission sources, atmospheric dispersion of emissions, implementation of abatement measures, integration with European-scale modelling, and environmental impacts. The model generates outputs from a national perspective which are used to evaluate alternative strategies in relation to emissions, deposition patterns, air quality metrics and ecosystem critical load exceedance. We present a selection of scenarios in relation to the 2020 Business-As-Usual projections and identify potential further reductions beyond those currently being planned.

  9. Cloud Feedbacks on Greenhouse Warming in a Multi-Scale Modeling Framework with a Higher-Order Turbulence Closure

    NASA Technical Reports Server (NTRS)

    Cheng, Anning; Xu, Kuan-Man

    2015-01-01

    Five-year simulation experiments with a multi-scale modeling Framework (MMF) with a advanced intermediately prognostic higher-order turbulence closure (IPHOC) in its cloud resolving model (CRM) component, also known as SPCAM-IPHOC (super parameterized Community Atmospheric Model), are performed to understand the fast tropical (30S-30N) cloud response to an instantaneous doubling of CO2 concentration with SST held fixed at present-day values. SPCAM-IPHOC has substantially improved the low-level representation compared with SPCAM. It is expected that the cloud responses to greenhouse warming in SPCAM-IPHOC is more realistic. The change of rising motion, surface precipitation, cloud cover, and shortwave and longwave cloud radiative forcing in SPCAM-IPHOC from the greenhouse warming will be presented in the presentation.

  10. Sparsity: a ubiquitous but unexplored property of geophysical signals for multi-scale modeling and reconstruction

    NASA Astrophysics Data System (ADS)

    Fouofula-Georgiou, E.; Ebtehaj, A. M.

    2012-04-01

    Sparsity: a ubiquitous but unexplored property of geophysical signals for multi-scale modeling and reconstruction Efi Foufoula-Georgiou and Ardeshir Mohammad Ebtehaj Department of Civil Engineering and National Center for Earth-surface Dynamics University of Minnesota, Minneapolis, MN 55414 Many geophysical processes exhibit variability over a wide range of scales. Yet, in numerical modeling or remote sensing observations not all of this variability is explicitly resolved due to limitations in computational resources or sensor configurations. As a result, sub-grid scale parameterizations and downscaling/upscaling representations are essential. Such representations take advantage of scale invariance which has been theoretically or empirically documented in a wide range of geophysical processes, including precipitation, soil moisture, and topography. Here we present a new direction in the field of multi-scale analysis and reconstruction. It capitalizes on the fact that most geophysical signals are naturally redundant, due to spatial dependence and coherence over a range of scales, and thus when projected onto an appropriate space (e.g, Fourier or wavelet) only a few representation coefficients are non-zero -- this property is called sparsity. The sparsity can serve as a priori knowledge to properly regularize the otherwise ill-posed inverse problem of creating information at scales smaller than resolved, which is at the heart of sub-grid scale and downscaling parameterizations. The same property of sparsity is also shown to play a revolutionary role in revisiting the problem of optimal estimation of non-Gaussian processes. Theoretical concepts are borrowed from the new field of compressive sampling and super-resolution and the merits of the methodology are demonstrated using examples from precipitation downscaling, multi-scale data fusion and data assimilation.

  11. Multi-scale plasticity modeling: Coupled discrete dislocation and continuum crystal plasticity

    NASA Astrophysics Data System (ADS)

    Wallin, M.; Curtin, W. A.; Ristinmaa, M.; Needleman, A.

    A hierarchical multi-scale model that couples a region of material described by discrete dislocation plasticity to a surrounding region described by conventional crystal plasticity is presented. The coupled model is aimed at capturing non-classical plasticity effects such as the long-range stresses associated with a density of geometrically necessary dislocations and source limited plasticity, while also accounting for plastic flow and the associated energy dissipation at much larger scales where such non-classical effects are absent. The key to the model is the treatment of the interface between the discrete and continuum regions, where continuity of tractions and displacements is maintained in an average sense and the flow of net Burgers vector is managed via "passing" of discrete dislocations. The formulation is used to analyze two plane strain problems: (i) tension of a block and (ii) crack growth under mode I loading with various sizes of the discrete dislocation plasticity region surrounding the crack tip. The computed crack growth resistance curves are nearly independent of the size of the discrete dislocation plasticity region for region sizes ranging from 30 μm×30 μm to 10 μm×5 μm. The multi-scale model can reduce the computational time for the mode I crack analysis by a factor of 14 with little or no loss of fidelity in the crack growth predictions.

  12. APPLICATION OF THE MODELS-3 COMMUNITY MULTI-SCALE AIR QUALITY (CMAQ) MODEL SYSTEM TO SOS/NASHVILLE 1999

    EPA Science Inventory

    The Models-3 Community Multi-scale Air Quality (CMAQ) model, first released by the USEPA in 1999 (Byun and Ching. 1999), continues to be developed and evaluated. The principal components of the CMAQ system include a comprehensive emission processor known as the Sparse Matrix O...

  13. 3D multi-scale modelling of mechanical behaviour of sound and leached mortar

    SciTech Connect

    Bernard, F.; Kamali-Bernard, S. Prince, W.

    2008-04-15

    A 3D multi-scale modelling of mechanical properties of cement-based materials approach is presented. The proposed approach provides a quantitative means to estimate and predict the mechanical properties of cement-based materials taking into account the eventual changes in the micro-structure. Two numerical tools are combined. First, the NIST's 3D model (CEMHYD3D) is used to generate a realistic 3D Representative Volume Element of cement-based materials at different scales. Then, multi-scale simulations are performed by using the FE software Abaqus for the calculation of the mechanical behaviour. The approach is then successfully applied to a specific mortar in order to determine firstly its mechanical behaviour under tensile and compression loadings and secondly the evolution of its Young's modulus under the leaching phenomenon. This evolution is a key parameter since the leaching may be critical for the mechanical integrity of concrete structures such as radioactive waste storage systems in which cement-based materials may be largely used. The numerical results of the modelling are consistent with the experimental ones.

  14. Advanced in situ multi-scale characterization of hardness of carbon-fiber-reinforced plastic

    NASA Astrophysics Data System (ADS)

    Wang, Hongxin; Masuda, Hideki; Kitazawa, Hideaki; Onishi, Keiko; Kawai, Masamichi; Fujita, Daisuke

    2016-10-01

    In situ multi-scale characterization of hardness of carbon-fiber-reinforced plastic (CFRP) is demonstrated by a traditional hardness tester, instrumented indentation tester and atomic-force-microscope (AFM)-based nanoindentation. In particular, due to the large residual indentation and nonuniform distribution of the microscale carbon fibers, the Vickers hardness could not be calculated by the traditional hardness tester. In addition, the clear residual microindentation could not be formed on the CFRP by instrumented indentation tester because of the large tip half angle of the Berkovich indenter. Therefore, an efficient technique for characterizing the true nanoscale hardness of CFRP was proposed and evaluated. The local hardness of the carbon fibers or plastic matrix on the nanoscale did not vary with nanoindentation location. The Vickers hardnesses of the carbon fiber and plastic matrix determined by AFM-based nanoindentation were 340 ± 30 and 40 ± 2 kgf/mm2, respectively.

  15. A Physiologically Based, Multi-Scale Model of Skeletal Muscle Structure and Function

    PubMed Central

    Röhrle, O.; Davidson, J. B.; Pullan, A. J.

    2012-01-01

    Models of skeletal muscle can be classified as phenomenological or biophysical. Phenomenological models predict the muscle’s response to a specified input based on experimental measurements. Prominent phenomenological models are the Hill-type muscle models, which have been incorporated into rigid-body modeling frameworks, and three-dimensional continuum-mechanical models. Biophysically based models attempt to predict the muscle’s response as emerging from the underlying physiology of the system. In this contribution, the conventional biophysically based modeling methodology is extended to include several structural and functional characteristics of skeletal muscle. The result is a physiologically based, multi-scale skeletal muscle finite element model that is capable of representing detailed, geometrical descriptions of skeletal muscle fibers and their grouping. Together with a well-established model of motor-unit recruitment, the electro-physiological behavior of single muscle fibers within motor units is computed and linked to a continuum-mechanical constitutive law. The bridging between the cellular level and the organ level has been achieved via a multi-scale constitutive law and homogenization. The effect of homogenization has been investigated by varying the number of embedded skeletal muscle fibers and/or motor units and computing the resulting exerted muscle forces while applying the same excitatory input. All simulations were conducted using an anatomically realistic finite element model of the tibialis anterior muscle. Given the fact that the underlying electro-physiological cellular muscle model is capable of modeling metabolic fatigue effects such as potassium accumulation in the T-tubular space and inorganic phosphate build-up, the proposed framework provides a novel simulation-based way to investigate muscle behavior ranging from motor-unit recruitment to force generation and fatigue. PMID:22993509

  16. Multi-scale Modeling in Biology: How to Bridge the Gaps between Scales?

    PubMed Central

    Qu, Zhilin; Garfinkel, Alan; Weiss, James N.; Nivala, Melissa

    2011-01-01

    Human physiological functions are regulated across many orders of magnitude in space and time. Integrating the information and dynamics from one scale to another is critical for the understanding of human physiology and the treatment of diseases. Multi-scale modeling, as a computational approach, has been widely adopted by researchers in computational and systems biology. A key unsolved issue is how to represent appropriately the dynamical behaviors of a high-dimensional model of a lower scale by a low-dimensional model of a higher scale, so that it can be used to investigate complex dynamical behaviors at even higher scales of integration. In the article, we first review the widely-used different modeling methodologies and their applications at different scales. We then discuss the gaps between different modeling methodologies and between scales, and discuss potential methods for bridging the gaps between scales. PMID:21704063

  17. Automatic Multi-Scale Calibration Procedure for Nested Hydrological-Hydrogeological Regional Models

    NASA Astrophysics Data System (ADS)

    Labarthe, B.; Abasq, L.; Flipo, N.; de Fouquet, C. D.

    2014-12-01

    Large hydrosystem modelling and understanding is a complex process depending on regional and local processes. A nested interface concept has been implemented in the hydrosystem modelling platform for a large alluvial plain model (300 km2) part of a 11000 km2 multi-layer aquifer system, included in the Seine basin (65000 km2, France). The platform couples hydrological and hydrogeological processes through four spatially distributed modules (Mass balance, Unsaturated Zone, River and Groundwater). An automatic multi-scale calibration procedure is proposed. Using different data sets from regional scale (117 gauging stations and 183 piezometers over the 65000 km2) to the intermediate scale(dense past piezometric snapshot), it permits the calibration and homogenization of model parameters over scales.The stepwise procedure starts with the optimisation of the water mass balance parameters at regional scale using a conceptual 7 parameters bucket model coupled with the inverse modelling tool PEST. The multi-objective function is derived from river discharges and their de-composition by hydrograph separation. The separation is performed at each gauging station using an automatic procedure based one Chapman filter. Then, the model is run at the regional scale to provide recharge estimate and regional fluxes to the groundwater local model. Another inversion method is then used to determine the local hydrodynamic parameters. This procedure used an initial kriged transmissivity field which is successively updated until the simulated hydraulic head distribution equals a reference one obtained by krigging. Then, the local parameters are upscaled to the regional model by renormalisation procedure.This multi-scale automatic calibration procedure enhances both the local and regional processes representation. Indeed, it permits a better description of local heterogeneities and of the associated processes which are transposed into the regional model, improving the overall performances

  18. Modelling strategies to predict the multi-scale effects of rural land management change

    NASA Astrophysics Data System (ADS)

    Bulygina, N.; Ballard, C. E.; Jackson, B. M.; McIntyre, N.; Marshall, M.; Reynolds, B.; Wheater, H. S.

    2011-12-01

    Changes to the rural landscape due to agricultural land management are ubiquitous, yet predicting the multi-scale effects of land management change on hydrological response remains an important scientific challenge. Much empirical research has been of little generic value due to inadequate design and funding of monitoring programmes, while the modelling issues challenge the capability of data-based, conceptual and physics-based modelling approaches. In this paper we report on a major UK research programme, motivated by a national need to quantify effects of agricultural intensification on flood risk. Working with a consortium of farmers in upland Wales, a multi-scale experimental programme (from experimental plots to 2nd order catchments) was developed to address issues of upland agricultural intensification. This provided data support for a multi-scale modelling programme, in which highly detailed physics-based models were conditioned on the experimental data and used to explore effects of potential field-scale interventions. A meta-modelling strategy was developed to represent detailed modelling in a computationally-efficient manner for catchment-scale simulation; this allowed catchment-scale quantification of potential management options. For more general application to data-sparse areas, alternative approaches were needed. Physics-based models were developed for a range of upland management problems, including the restoration of drained peatlands, afforestation, and changing grazing practices. Their performance was explored using literature and surrogate data; although subject to high levels of uncertainty, important insights were obtained, of practical relevance to management decisions. In parallel, regionalised conceptual modelling was used to explore the potential of indices of catchment response, conditioned on readily-available catchment characteristics, to represent ungauged catchments subject to land management change. Although based in part on

  19. Infrared/laser multi-sensor fusion and tracking based on the multi-scale model

    NASA Astrophysics Data System (ADS)

    Wang, Bingjian; Hao, Jingya; Yi, Xiang; Wu, Feihong; Li, Min; Qin, Hanlin; Huang, Hanqiao

    2016-03-01

    The state estimation problem of targets detected by infrared/laser composite detection system with different sampling rates was studied in this paper. An effective state estimation algorithm based on data fusion is presented. Because sampling rate of infrared detection system is much higher than that of the laser detection system, the theory of multi-scale analysis is used to establish multi-scale model in this algorithm. At the fine scale, angle information provided by infrared detection system is used to estimate the target state through the unscented Kalman filter. It makes full use of the high frequency characteristic of infrared detection system to improve target state estimation accuracy. At the coarse scale, due to the sampling ratio of infrared and laser detection systems is an integer multiple, the angle information can be fused directly with the distance information of laser detection system to determine the target location. The fused information is served as observation, while the converted measurement Kalman filter (CMKF) is used to estimate the target state, which greatly reduces the complexity of filtering process and gets the optimal fusion estimation. The simulation results of tracking a target in 3-D space by infrared and laser detection systems demonstrate that the proposed algorithm in this paper is efficient and can obtain better performance than traditional algorithm.

  20. Multi-scale quantum point contact model for filamentary conduction in resistive random access memories devices

    SciTech Connect

    Lian, Xiaojuan Cartoixà, Xavier; Miranda, Enrique; Suñé, Jordi; Perniola, Luca; Rurali, Riccardo; Long, Shibing; Liu, Ming

    2014-06-28

    We depart from first-principle simulations of electron transport along paths of oxygen vacancies in HfO{sub 2} to reformulate the Quantum Point Contact (QPC) model in terms of a bundle of such vacancy paths. By doing this, the number of model parameters is reduced and a much clearer link between the microscopic structure of the conductive filament (CF) and its electrical properties can be provided. The new multi-scale QPC model is applied to two different HfO{sub 2}-based devices operated in the unipolar and bipolar resistive switching (RS) modes. Extraction of the QPC model parameters from a statistically significant number of CFs allows revealing significant structural differences in the CF of these two types of devices and RS modes.

  1. Multi-Scale Modeling of Liquid Phase Sintering Affected by Gravity: Preliminary Analysis

    NASA Technical Reports Server (NTRS)

    Olevsky, Eugene; German, Randall M.

    2012-01-01

    A multi-scale simulation concept taking into account impact of gravity on liquid phase sintering is described. The gravity influence can be included at both the micro- and macro-scales. At the micro-scale, the diffusion mass-transport is directionally modified in the framework of kinetic Monte-Carlo simulations to include the impact of gravity. The micro-scale simulations can provide the values of the constitutive parameters for macroscopic sintering simulations. At the macro-scale, we are attempting to embed a continuum model of sintering into a finite-element framework that includes the gravity forces and substrate friction. If successful, the finite elements analysis will enable predictions relevant to space-based processing, including size and shape and property predictions. Model experiments are underway to support the models via extraction of viscosity moduli versus composition, particle size, heating rate, temperature and time.

  2. Multi-scale modeling of inter-granular fracture in UO2

    SciTech Connect

    Chakraborty, Pritam; Zhang, Yongfeng; Tonks, Michael R.; Biner, S. Bulent

    2015-03-01

    A hierarchical multi-scale approach is pursued in this work to investigate the influence of porosity, pore and grain size on the intergranular brittle fracture in UO2. In this approach, molecular dynamics simulations are performed to obtain the fracture properties for different grain boundary types. A phase-field model is then utilized to perform intergranular fracture simulations of representative microstructures with different porosities, pore and grain sizes. In these simulations the grain boundary fracture properties obtained from molecular dynamics simulations are used. The responses from the phase-field fracture simulations are then fitted with a stress-based brittle fracture model usable at the engineering scale. This approach encapsulates three different length and time scales, and allows the development of microstructurally informed engineering scale model from properties evaluated at the atomistic scale.

  3. On the mass-coupling relation of multi-scale quantum integrable models

    NASA Astrophysics Data System (ADS)

    Bajnok, Zoltán; Balog, János; Ito, Katsushi; Satoh, Yuji; Tóth, Gábor Zsolt

    2016-06-01

    We determine exactly the mass-coupling relation for the simplest multi-scale quantum integrable model, the homogenous sine-Gordon model with two independent mass-scales. We first reformulate its perturbed coset CFT description in terms of the perturbation of a projected product of minimal models. This representation enables us to identify conserved tensor currents on the UV side. These UV operators are then mapped via form factor perturbation theory to operators on the IR side, which are characterized by their form factors. The relation between the UV and IR operators is given in terms of the sought-for mass-coupling relation. By generalizing the Θ sum rule Ward identity we are able to derive differential equations for the mass-coupling relation, which we solve in terms of hypergeometric functions. We check these results against the data obtained by numerically solving the thermodynamic Bethe Ansatz equations, and find a complete agreement.

  4. Understanding Prairie Fen Hydrology - a Hierarchical Multi-Scale Groundwater Modeling Approach

    NASA Astrophysics Data System (ADS)

    Sampath, P.; Liao, H.; Abbas, H.; Ma, L.; Li, S.

    2012-12-01

    Prairie fens provide critical habitat to more than 50 rare species and significantly contribute to the biodiversity of the upper Great Lakes region. The sustainability of these globally unique ecosystems, however, requires that they be fed by a steady supply of pristine, calcareous groundwater. Understanding the hydrology that supports the existence of such fens is essential in preserving these valuable habitats. This research uses process-based multi-scale groundwater modeling for this purpose. Two fen-sites, MacCready Fen and Ives Road Fen, in Southern Michigan were systematically studied. A hierarchy of nested steady-state models was built for each fen-site to capture the system's dynamics at spatial scales ranging from the regional groundwater-shed to the local fens. The models utilize high-resolution Digital Elevation Models (DEM), National Hydrologic Datasets (NHD), a recently-assembled water-well database, and results from a state-wide groundwater mapping project to represent the complex hydro-geological and stress framework. The modeling system simulates both shallow glacial and deep bedrock aquifers as well as the interaction between surface water and groundwater. Aquifer heterogeneities were explicitly simulated with multi-scale transition probability geo-statistics. A two-way hydraulic head feedback mechanism was set up between the nested models, such that the parent models provided boundary conditions to the child models, and in turn the child models provided local information to the parent models. A hierarchical mass budget analysis was performed to estimate the seepage fluxes at the surface water/groundwater interfaces and to assess the relative importance of the processes at multiple scales that contribute water to the fens. The models were calibrated using observed base-flows at stream gauging stations and/or static water levels at wells. Three-dimensional particle tracking was used to predict the sources of water to the fens. We observed from the

  5. Fractional-order elastic models of cartilage: A multi-scale approach

    NASA Astrophysics Data System (ADS)

    Magin, Richard L.; Royston, Thomas J.

    2010-03-01

    The objective of this research is to develop new quantitative methods to describe the elastic properties (e.g., shear modulus, viscosity) of biological tissues such as cartilage. Cartilage is a connective tissue that provides the lining for most of the joints in the body. Tissue histology of cartilage reveals a multi-scale architecture that spans a wide range from individual collagen and proteoglycan molecules to families of twisted macromolecular fibers and fibrils, and finally to a network of cells and extracellular matrix that form layers in the connective tissue. The principal cells in cartilage are chondrocytes that function at the microscopic scale by creating nano-scale networks of proteins whose biomechanical properties are ultimately expressed at the macroscopic scale in the tissue's viscoelasticity. The challenge for the bioengineer is to develop multi-scale modeling tools that predict the three-dimensional macro-scale mechanical performance of cartilage from micro-scale models. Magnetic resonance imaging (MRI) and MR elastography (MRE) provide a basis for developing such models based on the nondestructive biomechanical assessment of cartilage in vitro and in vivo. This approach, for example, uses MRI to visualize developing proto-cartilage structure, MRE to characterize the shear modulus of such structures, and fractional calculus to describe the dynamic behavior. Such models can be extended using hysteresis modeling to account for the non-linear nature of the tissue. These techniques extend the existing computational methods to predict stiffness and strength, to assess short versus long term load response, and to measure static versus dynamic response to mechanical loads over a wide range of frequencies (50-1500 Hz). In the future, such methods can perhaps be used to help identify early changes in regenerative connective tissue at the microscopic scale and to enable more effective diagnostic monitoring of the onset of disease.

  6. Multi-scale process and supply chain modelling: from lignocellulosic feedstock to process and products.

    PubMed

    Hosseini, Seyed Ali; Shah, Nilay

    2011-04-01

    There is a large body of literature regarding the choice and optimization of different processes for converting feedstock to bioethanol and bio-commodities; moreover, there has been some reasonable technological development in bioconversion methods over the past decade. However, the eventual cost and other important metrics relating to sustainability of biofuel production will be determined not only by the performance of the conversion process, but also by the performance of the entire supply chain from feedstock production to consumption. Moreover, in order to ensure world-class biorefinery performance, both the network and the individual components must be designed appropriately, and allocation of resources over the resulting infrastructure must effectively be performed. The goal of this work is to describe the key challenges in bioenergy supply chain modelling and then to develop a framework and methodology to show how multi-scale modelling can pave the way to answer holistic supply chain questions, such as the prospects for second generation bioenergy crops.

  7. Validation of Multi-Scale Simulations of the Flow over Big Southern Butte Using Weather Research and Forecasting Model

    NASA Astrophysics Data System (ADS)

    Kosovic, B.; Jimenez, P. A.

    2015-12-01

    Advances in high performance computational resources and frameworks now make possible the use of Numerical Weather Predication (NWP) models for high-resolution simulations of atmospheric flows. In order to develop best practices, standards, and procedures for multi-scale simulations, we need to carry out extensive validation of NWP models across unprecedented range of scales from hundreds of kilometers to tens of meters. However, there are limited observational data available for evaluating high-resolution models. Recently, Nunalee et al (2015) validated large-eddy simulations (LES) using WRF for flow and dispersion based on the Cinder Cone Butte experiment carried out in Idaho in 1982. This study involved moderately complex terrain. We now extend the study to a significantly more complex terrain based on a more recent field study in Idaho. This field study include two experiments: the first one carried out in 2010 and centered on the Big Southern Butte (BSB) and the second in 2011 centered on the Salmon River Canyon both in Idaho (Butler et al., 2015). As a first step, here we focus on using the observations from the BSB experiment to validate multi-scale simulations using the WRF model. We carry out both mesoscale simulations and large-eddy simulations (LES). Nested mesoscale simulations are carried out using the innermost nest with grid cell size of 300m while nested WRF-LES are carried with grid cell size of ~50m. We analyze the performance of PBL scheme in mesoscale simulations and the resulting interplay between subgrid parameterization and numerical advection scheme in LES. The results of this analysis are used to assess performance of PBL schemes in complex terrain where the assumption of horizontal homogeneity on which these schemes are based are violated and to suggest the modifications to PBL scheme to account for the effect of heterogeneity.

  8. Evaluation and improvement of the cloud resolving model component of the multi-scale modeling framework

    SciTech Connect

    Xu, Kuan-Man; Cheng, Anning

    2009-10-01

    Developed, implemented and tested an improved Colorado State University (CSU) SAM (System for Atmospheric Modeling) cloud-resolving model (CRM) with the advanced third-order turbulence closure (IPHOC).

  9. Land-Atmosphere Coupling in the Multi-Scale Modelling Framework

    NASA Astrophysics Data System (ADS)

    Kraus, P. M.; Denning, S.

    2015-12-01

    The Multi-Scale Modeling Framework (MMF), in which cloud-resolving models (CRMs) are embedded within general circulation model (GCM) gridcells to serve as the model's cloud parameterization, has offered a number of benefits to GCM simulations. The coupling of these cloud-resolving models directly to land surface model instances, rather than passing averaged atmospheric variables to a single instance of a land surface model, the logical next step in model development, has recently been accomplished. This new configuration offers conspicuous improvements to estimates of precipitation and canopy through-fall, but overall the model exhibits warm surface temperature biases and low productivity.This work presents modifications to a land-surface model that take advantage of the new multi-scale modeling framework, and accommodate the change in spatial scale from a typical GCM range of ~200 km to the CRM grid-scale of 4 km.A parameterization is introduced to apportion modeled surface radiation into direct-beam and diffuse components. The diffuse component is then distributed among the land-surface model instances within each GCM cell domain. This substantially reduces the number excessively low light values provided to the land-surface model when cloudy conditions are modeled in the CRM, associated with its 1-D radiation scheme. The small spatial scale of the CRM, ~4 km, as compared with the typical ~200 km GCM scale, provides much more realistic estimates of precipitation intensity, this permits the elimination of a model parameterization of canopy through-fall. However, runoff at such scales can no longer be considered as an immediate flow to the ocean. Allowing sub-surface water flow between land-surface instances within the GCM domain affords better realism and also reduces temperature and productivity biases.The MMF affords a number of opportunities to land-surface modelers, providing both the advantages of direct simulation at the 4 km scale and a much reduced

  10. Optimal design of laminated-MRE bearings with multi-scale model

    NASA Astrophysics Data System (ADS)

    Chen, Shiwei; Wang, Xiaojie; Zhang, Ze; Mu, Wenjun; Li, Rui

    2016-10-01

    In the design of a laminated magneto-rheological elastomeric bearing (MREB), the passive rubbers are replaced with composite layers of rubber and MREs. The applied magnetic field, produced by the built-in electromagnet through the input current, changes the stiffness and damping of MREs, and thus that of the device. Typically, a good MREB should possess higher adjustable properties with less activating power in avoiding overheating problem. Thus an optimized design of MREB should integrate the MRE material design into mechanical and electromagnetic components to achieve a trade-off between power consumption and adjustability of stiffness. In this study, we propose a method to analyze and design a laminated MRE bearing, in which the optimal parameters of materials and mechanical structure of the MRE bearing are determined. Based on the multi-scale and magneto-mechanical coupling theories, we establish a multi-scale model for the MRE bearing considering the influence of particle volume fraction, particle distribution, and thickness of MRE laminated layers on its mechanical performance. Within the micro-scale analysis, the representative volume unit is used to address the effect of particle volume fraction and distribution on mechanical and magnetic properties of MRE itself. Within the macro-scale analysis, we build both mechanical and magnetic models for the laminated MRE bearing. Based on the theoretical analysis, a laminated MRE bearing with four-layer MRE is designed and fabricated. The performance of the MRE bearing has been tested by using MTS test bench. The results are compared with that of model analysis. Both experimental and theoretical results indicate that optimal design of MREB depends on the MRE’s particle volume fraction which is related with MREB’s input power limitation.

  11. Multi-scale model analysis and hindcast of the 2013 Colorado Flood

    NASA Astrophysics Data System (ADS)

    Gochis, David; Yu, Wei; Sampson, Kevin; Dugger, Aubrey; McCreight, James; Zhang, Yongxin; Ikeda, Kyoko

    2015-04-01

    While the generation of most flood and flash flood events is fundamentally linked to the occurrence of heavy rainfall, the physical mechanisms responsible for translating rainfall into floods are complex and manifold. These runoff generation processes evolve over many spatial and temporal scales during the course of flooding events. As such robust flood and flash flood prediction systems need to account for multitude of terrestrial processes occurring over a wide range of space and time scales. One such extreme multiscale flood event was the 2013 Colorado Flood in which over 400 mm of rainfall fell along the Rock Mountain mountain front region over the course of a few days. The flooding impacts from this heavy rainfall event included not only high, fast flows in steep mountain streams but also included large areas of inundation on the adjacent plains and numerous soil saturation excess impacts such as hillslope failures and groundwater intrusions into domestic structures. A multi-scale and multi-process evaluation of this flood event is performed using the community WRF-Hydro modeling system. We incorporate several operational quantitative precipitation estimate and quantitative precipitation forecast products in the analysis and document the skill of multiple configurations of WRF-Hydro physics options across a range of contributing area length scales. Emphasis is placed on assessing how well the different model configurations capture the multi-scale streamflow response from small headwater catchments out to the entire South Platte River basin whose total contributing area exceeds 25,000 sq km. In addition to streamflow we also present evaluations of event simulations and hindcasts of soil saturation fraction, groundwater levels and inundated areas as a means of assessing different runoff generation mechanisms. Finally, results from a U.S. national-scale, fully-coupled hydrometeorological hindcast of the 2013 Colorado flood event using the combined WRF atmospheric

  12. The NCEP Eulerian Non-hydrostatic Multi-scale Model (NMMB)

    NASA Astrophysics Data System (ADS)

    Janjic, Z.; Vasic, R.; Djurdjevic, V.; Black, T.; Jovic, D.

    2014-12-01

    The unified Non-hydrostatic Multi-scale Model (NMMB) is being developed at the National Centers for Environmental Predictions. The model dynamics preserve a number of important properties of differential operators and conserve a variety of first order and quadratic quantities. The nonlinear dynamics is controlled by conserving energy and enstrophy in case of non-divergent flow. Over-specification of non-hydrostatic vertical velocity is avoided. The physical package was developed from the WRF NMM's physics, but other physics options are also available. The regional version of the NMMB is run operationally as the main deterministic North American short-range forecasting model (NAM) and in a number of other applications. The global NMMB also has been run over the last few years experimentally in order to assess its capabilities and develop it further. In terms of large scale metrics, the performance of the global NMMB in medium range weather forecasting has been generally comparable to that of other major medium range forecasting systems. Its computational efficiency satisfies and exceeds the current and projected operational requirements. Recently, the transition has started of the operational hurricane forecasting system HWRF from the WRF NMM dynamics to those of the NMMB. This system involves the use of a hierarchy of 2-way interactive telescoping moving nests. The work on developing a unified multi-scale physics package has continued. Extended range forecasts showed large sensitivity to the method for representing clouds. With the clouds represented by optical properties of their microphysics species, the results depend on the microphysics scheme used. Also, taking into account the impact of convective clouds remains a challenge with this approach. Numerous sensitivity studies of physical parameterizations and the dynamical core features have been carried out as well. Relevant results will be presented and discussed, including some results of recent idealized

  13. Multi-scale model for the hierarchical architecture of native cellulose hydrogels.

    PubMed

    Martínez-Sanz, Marta; Mikkelsen, Deirdre; Flanagan, Bernadine; Gidley, Michael J; Gilbert, Elliot P

    2016-08-20

    The structure of protiated and deuterated cellulose hydrogels has been investigated using a multi-technique approach combining small-angle scattering with diffraction, spectroscopy and microscopy. A model for the multi-scale structure of native cellulose hydrogels is proposed which highlights the essential role of water at different structural levels characterised by: (i) the existence of cellulose microfibrils containing an impermeable crystalline core surrounded by a partially hydrated paracrystalline shell, (ii) the creation of a strong network of cellulose microfibrils held together by hydrogen bonding to form cellulose ribbons and (iii) the differential behaviour of tightly bound water held within the ribbons compared to bulk solvent. Deuterium labelling provides an effective platform on which to further investigate the role of different plant cell wall polysaccharides in cellulose composite formation through the production of selectively deuterated cellulose composite hydrogels. PMID:27178962

  14. Indicator mining model for spatial multi-scale degraded land evaluation

    NASA Astrophysics Data System (ADS)

    Liu, Dianfeng; Liu, Yaolin; Xia, Yin; Hong, Xiaofeng; Zhao, Zhongjun

    2009-10-01

    At present, no feasible and effective methods meet the requirements of constructing a comprehensive and representative indicator system for degraded land evaluation, which orients spatial multi-scale and diversity of evaluation objects as well as integrates experts' judgments and objective information. This paper, tying to solve the problem, firstly proposes three propositions on evaluation indicator knowledge base (EIKB), universe evaluation indicator set (UEIS), evaluation indicator subset (EIS) and Mapping Rule of EIS (MREIS), and then constructs an heuristic indicator mining model (HIMM) based on above theories, variable precision rough set and information entropy. Finally, we applied HIMM to practical degraded land evaluation and examined the effectiveness of HIMM. The result shows that HIMM is applicable, especially in the aspect of solving the comprehensive and representative problem in the process of indicator system construction.

  15. CMAQ (Community Multi-Scale Air Quality) atmospheric distribution model adaptation to region of Hungary

    NASA Astrophysics Data System (ADS)

    Lázár, Dóra; Weidinger, Tamás

    2016-04-01

    For our days, it has become important to measure and predict the concentration of harmful atmospheric pollutants such as dust, aerosol particles of different size ranges, nitrogen compounds, and ozone. The Department of Meteorology at Eötvös Loránd University has been applying the WRF (Weather Research and Forecasting) model several years ago, which is suitable for weather forecasting tasks and provides input data for various environmental models (e.g. DNDC). By adapting the CMAQ (Community Multi-scale Air Quality) model we have designed a combined ambient air-meteorological model (WRF-CMAQ). In this research it is important to apply different emission databases and a background model describing the initial distribution of the pollutant. We used SMOKE (Sparse Matrix Operator Kernel Emissions) model for construction emission dataset from EMEP (European Monitoring and Evaluation Programme) inventories and GEOS-Chem model for initial and boundary conditions. Our model settings were CMAQ CB05 (Carbon Bond 2005) chemical mechanism with 108 x 108 km, 36 x 36 km and 12 x 12 km grids for regions of Europe, the Carpathian Basin and Hungary respectively. i) The structure of the model system, ii) a case study for Carpathian Basin (an anticyclonic weather situation at 21th September 2012) are presented. iii) Verification of ozone forecast has been provided based on the measurements of background air pollution stations. iv) Effects of model attributes (f.e. transition time, emission dataset, parameterizations) for the ozone forecast in Hungary are also investigated.

  16. Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems

    PubMed Central

    Cilfone, Nicholas A.; Kirschner, Denise E.; Linderman, Jennifer J.

    2015-01-01

    Biologically related processes operate across multiple spatiotemporal scales. For computational modeling methodologies to mimic this biological complexity, individual scale models must be linked in ways that allow for dynamic exchange of information across scales. A powerful methodology is to combine a discrete modeling approach, agent-based models (ABMs), with continuum models to form hybrid models. Hybrid multi-scale ABMs have been used to simulate emergent responses of biological systems. Here, we review two aspects of hybrid multi-scale ABMs: linking individual scale models and efficiently solving the resulting model. We discuss the computational choices associated with aspects of linking individual scale models while simultaneously maintaining model tractability. We demonstrate implementations of existing numerical methods in the context of hybrid multi-scale ABMs. Using an example model describing Mycobacterium tuberculosis infection, we show relative computational speeds of various combinations of numerical methods. Efficient linking and solution of hybrid multi-scale ABMs is key to model portability, modularity, and their use in understanding biological phenomena at a systems level. PMID:26366228

  17. Towards Characterization, Modeling, and Uncertainty Quantification in Multi-scale Mechanics of Oragnic-rich Shales

    NASA Astrophysics Data System (ADS)

    Abedi, S.; Mashhadian, M.; Noshadravan, A.

    2015-12-01

    Increasing the efficiency and sustainability in operation of hydrocarbon recovery from organic-rich shales requires a fundamental understanding of chemomechanical properties of organic-rich shales. This understanding is manifested in form of physics-bases predictive models capable of capturing highly heterogeneous and multi-scale structure of organic-rich shale materials. In this work we present a framework of experimental characterization, micromechanical modeling, and uncertainty quantification that spans from nanoscale to macroscale. Application of experiments such as coupled grid nano-indentation and energy dispersive x-ray spectroscopy and micromechanical modeling attributing the role of organic maturity to the texture of the material, allow us to identify unique clay mechanical properties among different samples that are independent of maturity of shale formations and total organic content. The results can then be used to inform the physically-based multiscale model for organic rich shales consisting of three levels that spans from the scale of elementary building blocks (e.g. clay minerals in clay-dominated formations) of organic rich shales to the scale of the macroscopic inorganic/organic hard/soft inclusion composite. Although this approach is powerful in capturing the effective properties of organic-rich shale in an average sense, it does not account for the uncertainty in compositional and mechanical model parameters. Thus, we take this model one step forward by systematically incorporating the main sources of uncertainty in modeling multiscale behavior of organic-rich shales. In particular we account for the uncertainty in main model parameters at different scales such as porosity, elastic properties and mineralogy mass percent. To that end, we use Maximum Entropy Principle and random matrix theory to construct probabilistic descriptions of model inputs based on available information. The Monte Carlo simulation is then carried out to propagate the

  18. multi-scale approaches for full waveform difference inversion and tomographic model analysis

    NASA Astrophysics Data System (ADS)

    Yuan, Y.; Simons, F. J.; Luo, Y.

    2012-12-01

    Tomographic Earth models are solutions to mixed-determined inverse problems, which are formulated to minimize some measure of difference between synthetics and observed data. Typically, the measurement takes the form of a cross-correlation travel-time difference, or it might be the norm of the difference between the entire waveforms, in which case every wiggle is being used to extract information from the data. Full-waveform difference tomography suffers from a slow convergence rate and a danger of converging to local minima. In this presentation, we explore several routes to improving full-waveform inversion strategies for global and regional seismic tomography. First, we will discuss a wavelet-based multi-scale approach that works progressively from low to higher scales, step-by-step involving more details of the waveform. Second, we will discuss a hybrid misfit strategy that combines cross-correlation traveltime and waveform-difference measurements. We will discuss the making of multiscale sensitivity kernels using wavelet decompositions of the seismogram. Lastly, we move to the model space to conduct a multi-scale analysis of global tomographic models using a class of 3-D spherical wavelet bases that are implemented on the ``cubed ball'', the 3-D extension of the ``cubed sphere''. Using this novel transform we study the sparsity of global seismic tomographic models via thresholded reconstruction, and characterize the relative importance and patterns of features in the Earth models via individual and cumulative reconstructions of their wavelet coefficients. Whether on the side of the data, the sensitivity kernels, or in the model space, tomographic inverse problems have much to gain from the flexibility of the wavelet decomposition in one, two and three dimensions, and this on a global, regional or exploration scale, as we show by example. Full waveform difference inversion. The first figure shows our target model with two anomalous regions. The red stars

  19. A multi scale multi-dimensional thermo electrochemical modelling of high capacity lithium-ion cells

    NASA Astrophysics Data System (ADS)

    Tourani, Abbas; White, Peter; Ivey, Paul

    2014-06-01

    Lithium iron phosphate (LFP) and lithium manganese oxide (LMO) are competitive and complementary to each other as cathode materials for lithium-ion batteries, especially for use in electric vehicles. A multi scale multi-dimensional physic-based model is proposed in this paper to study the thermal behaviour of the two lithium-ion chemistries. The model consists of two sub models, a one dimensional (1D) electrochemical sub model and a two dimensional (2D) thermo-electric sub model, which are coupled and solved concurrently. The 1D model predicts the heat generation rate (Qh) and voltage (V) of the battery cell through different load cycles. The 2D model of the battery cell accounts for temperature distribution and current distribution across the surface of the battery cell. The two cells are examined experimentally through 90 h load cycles including high/low charge/discharge rates. The experimental results are compared with the model results and they are in good agreement. The presented results in this paper verify the cells temperature behaviour at different operating conditions which will lead to the design of a cost effective thermal management system for the battery pack.

  20. Multi-scale modeling of urban air pollution: development of a Street-in-Grid model

    NASA Astrophysics Data System (ADS)

    Kim, Youngseob; Wu, You; Seigneur, Christian; Roustan, Yelva

    2016-04-01

    A new multi-scale model of urban air pollution is presented. This model combines a chemical-transport model (CTM) that includes a comprehensive treatment of atmospheric chemistry and transport at spatial scales greater than 1 km and a street-network model that describes the atmospheric concentrations of pollutants in an urban street network. The street-network model is based on the general formulation of the SIRANE model and consists of two main components: a street-canyon component and a street-intersection component. The street-canyon component calculates the mass transfer velocity at the top of the street canyon (roof top) and the mean wind velocity within the street canyon. The estimation of the mass transfer velocity depends on the intensity of the standard deviation of the vertical velocity at roof top. The effect of various formulations of this mass transfer velocity on the pollutant transport at roof-top level is examined. The street-intersection component calculates the mass transfer from a given street to other streets across the intersection. These mass transfer rates among the streets are calculated using the mean wind velocity calculated for each street and are balanced so that the total incoming flow rate is equal to the total outgoing flow rate from the intersection including the flow between the intersection and the overlying atmosphere at roof top. In the default option, the Leighton photostationary cycle among ozone (O3) and nitrogen oxides (NO and NO2) is used to represent the chemical reactions within the street network. However, the influence of volatile organic compounds (VOC) on the pollutant concentrations increases when the nitrogen oxides (NOx) concentrations are low. To account for the possible VOC influence on street-canyon chemistry, the CB05 chemical kinetic mechanism, which includes 35 VOC model species, is implemented in this street-network model. A sensitivity study is conducted to assess the uncertainties associated with the use of

  1. An Eye Model for Computational Dosimetry Using A Multi-Scale Voxel Phantom

    NASA Astrophysics Data System (ADS)

    Caracappa, Peter F.; Rhodes, Ashley; Fiedler, Derek

    2014-06-01

    The lens of the eye is a radiosensitive tissue with cataract formation being the major concern. Recently reduced recommended dose limits to the lens of the eye have made understanding the dose to this tissue of increased importance. Due to memory limitations, the voxel resolution of computational phantoms used for radiation dose calculations is too large to accurately represent the dimensions of the eye. A revised eye model is constructed using physiological data for the dimensions of radiosensitive tissues, and is then transformed into a high-resolution voxel model. This eye model is combined with an existing set of whole body models to form a multi-scale voxel phantom, which is used with the MCNPX code to calculate radiation dose from various exposure types. This phantom provides an accurate representation of the radiation transport through the structures of the eye. Two alternate methods of including a high-resolution eye model within an existing whole body model are developed. The accuracy and performance of each method is compared against existing computational phantoms.

  2. Deconvolution of Poisson-Limited Data Using a Bayesian Multi-Scale Model

    NASA Astrophysics Data System (ADS)

    Kolaczyk, E. D.; Nowak, R. D.

    1999-04-01

    We present a new approach for producing deconvolved spectra and images, based on a novel non-parametric, multi-scale statistical model designed explicitly for Poisson limited data. The framework within which we work is completely general, requiring only that the user specify the manner in which the data were ``blurred'' (for example, through an instrument-specific PSF). Therefore, we anticipate our method serving in problems involving data at any of a variety of energies, especially at the x-ray and gamma-ray levels, for deconvolution problems arising in a variety of missions -- particularly when there is not yet a good analytical model for the source(s). The underlying statistical framework explicitly models the process of (dis)aggregating counts across multiple resolutions. The result is a multi-scale (though not wavelet-based) representation of the source object to be recovered through the deconvolution. Furthermore, this framework is built completely within the context of the original Poisson data likelihood, so that we proceed without the use of statistical approximations (such as chi (2) approximations) or data transformations. Adopting a Bayesian paradigm, a flexible prior probability structure is used to regularize the set of possible solutions to what is formally a statistical inverse problem. This prior is both intuitive and interpretable, in that it models the degree to which counts are allowed to be (dis)aggregated at each location-scale combination. Estimates of the ``deblurred'' source object are obtained in our procedure using standard Bayesian statistical techniques (i.e., based on the mode of the posterior distribution of the object given the data). Despite the generality of this method and the potentially complex structures that may be modeled, these estimates may be produced using an efficient iterative algorithm (i.e., the expectation-maximization (EM) algorithm), wherein iterates at each stage are yielded by closed-form solutions to simple

  3. A multi-scale modelling procedure to quantify hydrological impacts of upland land management

    NASA Astrophysics Data System (ADS)

    Wheater, H. S.; Jackson, B.; Bulygina, N.; Ballard, C.; McIntyre, N.; Marshall, M.; Frogbrook, Z.; Solloway, I.; Reynolds, B.

    2008-12-01

    Recent UK floods have focused attention on the effects of agricultural intensification on flood risk. However, quantification of these effects raises important methodological issues. Catchment-scale data have proved inadequate to support analysis of impacts of land management change, due to climate variability, uncertainty in input and output data, spatial heterogeneity in land use and lack of data to quantify historical changes in management practices. Manipulation experiments to quantify the impacts of land management change have necessarily been limited and small scale, and in the UK mainly focused on the lowlands and arable agriculture. There is a need to develop methods to extrapolate from small scale observations to predict catchment-scale response, and to quantify impacts for upland areas. With assistance from a cooperative of Welsh farmers, a multi-scale experimental programme has been established at Pontbren, in mid-Wales, an area of intensive sheep production. The data have been used to support development of a multi-scale modelling methodology to assess impacts of agricultural intensification and the potential for mitigation of flood risk through land use management. Data are available from replicated experimental plots under different land management treatments, from instrumented field and hillslope sites, including tree shelter belts, and from first and second order catchments. Measurements include climate variables, soil water states and hydraulic properties at multiple depths and locations, tree interception, overland flow and drainflow, groundwater levels, and streamflow from multiple locations. Fine resolution physics-based models have been developed to represent soil and runoff processes, conditioned using experimental data. The detailed models are used to calibrate simpler 'meta- models' to represent individual hydrological elements, which are then combined in a semi-distributed catchment-scale model. The methodology is illustrated using field

  4. On the computation of a retina resistivity profile for applications in multi-scale modeling of electrical stimulation and absorption

    NASA Astrophysics Data System (ADS)

    Loizos, Kyle; RamRakhyani, Anil Kumar; Anderson, James; Marc, Robert; Lazzi, Gianluca

    2016-06-01

    This study proposes a methodology for computationally estimating resistive properties of tissue in multi-scale computational models, used for studying the interaction of electromagnetic fields with neural tissue, with applications to both dosimetry and neuroprosthetics. Traditionally, models at bulk tissue- and cellular-level scales are solved independently, linking resulting voltage from existing resistive tissue-scale models as extracellular sources to cellular models. This allows for solving the effects that external electric fields have on cellular activity. There are two major limitations to this approach: first, the resistive properties of the tissue need to be chosen, of which there are contradicting measurements in literature; second, the measurements of resistivity themselves may be inaccurate, leading to the mentioned contradicting results found across different studies. Our proposed methodology allows for constructing computed resistivity profiles using knowledge of only the neural morphology within the multi-scale model, resulting in a practical implementation of the effective medium theory; this bypasses concerns regarding the choice of resistive properties and accuracy of measurement setups. A multi-scale model of retina is constructed with an external electrode to serve as a test bench for analyzing existing and resulting resistivity profiles, and validation is presented through the reconstruction of a published resistivity profile of retina tissue. Results include a computed resistivity profile of retina tissue for use with a retina multi-scale model used to analyze effects of external electric fields on neural activity.

  5. On the computation of a retina resistivity profile for applications in multi-scale modeling of electrical stimulation and absorption

    PubMed Central

    Loizos, Kyle; RamRakhyani, Anil Kumar; Anderson, James; Marc, Robert; Lazzi, Gianluca

    2016-01-01

    This study proposes a methodology for computationally estimating resistive properties of tissue in multi-scale computational models, used for studying the interaction of electromagnetic fields with neural tissue, with applications to both dosimetry and neuroprosthetics. Traditionally, models at bulk tissue- and cellular-level scales are solved independently, linking resulting voltage from existing resistive tissue-scale models as extracellular sources to cellular models. This allows for solving the effects that external electric fields have on cellular activity. There are two major limitations to this approach: first, the resistive properties of the tissue need to be chosen, of which there are contradicting measurements in literature; second, the measurements of resistivity themselves may be inaccurate, leading to the mentioned contradicting results found across different studies. Our proposed methodology allows for constructing computed resistivity profiles using knowledge of only the neural morphology within the multi-scale model, resulting in a practical implementation of the effective medium theory; this bypasses concerns regarding the choice of resistive properties and accuracy of measurement setups. A multi-scale model of retina is constructed with an external electrode to serve as a test bench for analyzing existing and resulting resistivity profiles, and validation is presented through the reconstruction of a published resistivity profile of retina tissue. Results include a computed resistivity profile of retina tissue for use with a retina multi-scale model used to analyze effects of external electric fields on neural activity. PMID:27223656

  6. Progression to multi-scale models and the application to food system intervention strategies.

    PubMed

    Gröhn, Yrjö T

    2015-02-01

    The aim of this article is to discuss how the systems science approach can be used to optimize intervention strategies in food animal systems. It advocates the idea that the challenges of maintaining a safe food supply are best addressed by integrating modeling and mathematics with biological studies critical to formulation of public policy to address these challenges. Much information on the biology and epidemiology of food animal systems has been characterized through single-discipline methods, but until now this information has not been thoroughly utilized in a fully integrated manner. The examples are drawn from our current research. The first, explained in depth, uses clinical mastitis to introduce the concept of dynamic programming to optimize management decisions in dairy cows (also introducing the curse of dimensionality problem). In the second example, a compartmental epidemic model for Johne's disease with different intervention strategies is optimized. The goal of the optimization strategy depends on whether there is a relationship between Johne's and Crohn's disease. If so, optimization is based on eradication of infection; if not, it is based on the cow's performance only (i.e., economic optimization, similar to the mastitis example). The third example focuses on food safety to introduce risk assessment using Listeria monocytogenes and Salmonella Typhimurium. The last example, practical interventions to effectively manage antibiotic resistance in beef and dairy cattle systems, introduces meta-population modeling that accounts for bacterial growth not only in the host (cow), but also in the cow's feed, drinking water and the housing environment. Each example stresses the need to progress toward multi-scale modeling. The article ends with examples of multi-scale systems, from food supply systems to Johne's disease. Reducing the consequences of foodborne illnesses (i.e., minimizing disease occurrence and associated costs) can only occur through an

  7. A semi-analytical model for the flow behavior of naturally fractured formations with multi-scale fracture networks

    NASA Astrophysics Data System (ADS)

    Jia, Pin; Cheng, Linsong; Huang, Shijun; Wu, Yonghui

    2016-06-01

    This paper presents a semi-analytical model for the flow behavior of naturally fractured formations with multi-scale fracture networks. The model dynamically couples an analytical dual-porosity model with a numerical discrete fracture model. The small-scale fractures with the matrix are idealized as a dual-porosity continuum and an analytical flow solution is derived based on source functions in Laplace domain. The large-scale fractures are represented explicitly as the major fluid conduits and the flow is numerically modeled, also in Laplace domain. This approach allows us to include finer details of the fracture network characteristics while keeping the computational work manageable. For example, the large-scale fracture network may have complex geometry and varying conductivity, and the computations can be done at predetermined, discrete times, without any grids in the dual-porosity continuum. The validation of the semi-analytical model is demonstrated in comparison to the solution of ECLIPSE reservoir simulator. The simulation is fast, gridless and enables rapid model setup. On the basis of the model, we provide detailed analysis of the flow behavior of a horizontal production well in fractured reservoir with multi-scale fracture networks. The study has shown that the system may exhibit six flow regimes: large-scale fracture network linear flow, bilinear flow, small-scale fracture network linear flow, pseudosteady-state flow, interporosity flow and pseudoradial flow. During the first four flow periods, the large-scale fracture network behaves as if it only drains in the small-scale fracture network; that is, the effect of the matrix is negligibly small. The characteristics of the bilinear flow and the small-scale fracture network linear flow are predominantly determined by the dimensionless large-scale fracture conductivity. And low dimensionless fracture conductivity will generate large pressure drops in the large-scale fractures surrounding the wellbore. With

  8. A Multi-scale Modeling System: Developments, Applications and Critical Issues

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo; Chern, Jiundar; Atlas, Robert; Randall, David; Lin, Xin; Khairoutdinov, Marat; Li, Jui-Lin; Waliser, Duane E.; Hou, Arthur; Peters-Lidard, Christa; Lau, William; Simpson, Joanne

    2006-01-01

    A multi-scale modeling framework (MMF), which replaces the conventional cloud parameterizations with a cloud-resolving model (CRM) in each grid column of a GCM, constitutes a new and promising approach. The MMF can provide for global coverage and two-way interactions between the CRMs and their parent GCM. The GCM allows global coverage and the CRM allows explicit simulation of cloud processes and their interactions with radiation and surface processes. A new MMF has been developed that is based the Goddard finite volume GCM (fvGCM) and the Goddard Cumulus Ensemble (GCE) model. This Goddard MMF produces many features that are similar to another MMF that was developed at Colorado State University (CSU), such as an improved .surface precipitation pattern, better cloudiness, improved diurnal variability over both oceans and continents, and a stronger, propagating Madden-Julian oscillation (MJO) compared to their parent GCMs using conventional cloud parameterizations. Both MMFs also produce a precipitation bias in the western Pacific during Northern Hemisphere summer. However, there are also notable differences between two MMFs. For example, the CSU MMF simulates less rainfall over land than its parent GCM. This is why the CSU MMF simulated less overall global rainfall than its parent GCM. The Goddard MMF overestimates global rainfall because of its oceanic component. Some critical issues associated with the Goddard MMF are presented in this paper.

  9. Multi-scale modelling of cancer cell intravasation: the role of cadherins in metastasis

    NASA Astrophysics Data System (ADS)

    Ramis-Conde, Ignacio; Chaplain, Mark A. J.; Anderson, Alexander R. A.; Drasdo, Dirk

    2009-03-01

    Transendothelial migration is a crucial process of the metastatic cascade in which a malignant cell attaches itself to the endothelial layer forming the inner wall of a blood or lymph vessel and creates a gap through which it enters into the bloodstream (or lymphatic system) and then is transported to distant parts of the body. In this process both biological pathways involving cell adhesion molecules such as VE-cadherin and N-cadherin, and the biophysical properties of the cells play an important role. In this paper, we present one of the first mathematical models considering the problem of cancer cell intravasation. We use an individual force-based multi-scale approach which accounts for intra- and inter-cellular protein pathways and for the physical properties of the cells, and a modelling framework which accounts for the biological shape of the vessel. Using our model, we study the influence of different protein pathways in the achievement of transendothelial migration and give quantitative simulation results comparable with real experiments.

  10. A multi-scale model for geared transmission aero-thermodynamics

    NASA Astrophysics Data System (ADS)

    McIntyre, Sean M.

    -steady cyclic-symmetric simulation of the internal flow. This high-frequency conduction solution is coupled directly with a model for the meshing friction, developed by a collaborator, which was adapted for use in a finite-volume CFD code. The local surface heat flux on solid surfaces is calculated by time-averaging the heat flux in the high-frequency analysis. This serves as a fixed-flux boundary condition in the long time scale conduction module. The temperature distribution from this long time scale heat transfer calculation serves as a boundary condition for the internal convection simulation, and as the initial condition for the high-frequency heat transfer module. Using this multi-scale model, simulations were performed for equilibrium and loss-of-lubrication operation of the NASA Glenn Research Center test stand. Results were compared with experimental measurements. In addition to the multi-scale model itself, several other specific contributions were made. Eulerian models for droplets and wall-films were developed and im- plemented in the CFD code. A novel approach to retaining liquid film on the solid surfaces, and strategies for its mass exchange with droplets, were developed and verified. Models for interfacial transfer between droplets and wall-film were implemented, and include the effects of droplet deposition, splashing, bouncing, as well as film breakup. These models were validated against airfoil data. To mitigate the observed slow convergence of CFD simulations of the enclosed aerodynamic flows within gearboxes, Fourier stability analysis was applied to the SIMPLE-C fractional-step algorithm. From this, recommendations to accelerate the convergence rate through enhanced pressure-velocity coupling were made. These were shown to be effective. A fast-running finite-volume reduced-order-model of the gearbox aero-thermo- dynamics was developed, and coupled with the tribology model to investigate the sensitivity of loss-of-lubrication predictions to various model

  11. Multi-scale models of grassland passerine abundance in a fragmented system in Wisconsin

    USGS Publications Warehouse

    Renfrew, R.B.; Ribic, C.A.

    2008-01-01

    Fragmentation of grasslands has been implicated in grassland bird population declines. Multi-scale models are being increasingly used to assess potential factors that influence grassland bird presence, abundance, and productivity. However, studies rarely assess fragmentation metrics, and seldom evaluate more than two scales or interactions among scales. We evaluated the relative importance of characteristics at multiple scales to patterns in relative abundance of Savannah Sparrow (Passerculus sandwichensis), Grasshopper Sparrow (Ammodramus savannarum), Eastern Meadowlark (Sturnella magna), and Bobolink (Dolichonyx oryzivorus). We surveyed birds in 74 southwestern Wisconsin pastures from 1997 to 1999 and compared models with explanatory variables from multiple scales: within-patch vegetation structure (microhabitat), patch (macrohabitat), and three landscape extents. We also examined interactions between macrohabitat and landscape factors. Core area of pastures was an important predictor of relative abundance, and composition of the landscape was more important than configuration. Relative abundance was frequently higher in pastures with more core area and in landscapes with more grassland and less wooded area. The direction and strength of the effect of core pasture size on relative abundance changed depending on amount of wooded area in the landscape. Relative abundance of grassland birds was associated with landscape variables more frequently at the 1200-m scale than at smaller scales. To develop better predictive models, parameters at multiple scales and their interactive effects should be included, and results should be evaluated in the context of microhabitat variability, landscape composition, and fragmentation in the study area. ?? 2007 Springer Science+Business Media B.V.

  12. Multi-scale process and supply chain modelling: from lignocellulosic feedstock to process and products

    PubMed Central

    Hosseini, Seyed Ali; Shah, Nilay

    2011-01-01

    There is a large body of literature regarding the choice and optimization of different processes for converting feedstock to bioethanol and bio-commodities; moreover, there has been some reasonable technological development in bioconversion methods over the past decade. However, the eventual cost and other important metrics relating to sustainability of biofuel production will be determined not only by the performance of the conversion process, but also by the performance of the entire supply chain from feedstock production to consumption. Moreover, in order to ensure world-class biorefinery performance, both the network and the individual components must be designed appropriately, and allocation of resources over the resulting infrastructure must effectively be performed. The goal of this work is to describe the key challenges in bioenergy supply chain modelling and then to develop a framework and methodology to show how multi-scale modelling can pave the way to answer holistic supply chain questions, such as the prospects for second generation bioenergy crops. PMID:22482032

  13. Kinetic Approaches to Shear-Driven Magnetic Reconnection for Multi-Scale Modeling of CME Initiation

    NASA Astrophysics Data System (ADS)

    Black, C.; Antiochos, S. K.; DeVore, C.; Germaschewski, K.; Karpen, J. T.

    2013-12-01

    In the standard model for coronal mass ejections (CME) and/or solar flares, the free energy for the event resides in the strongly sheared magnetic field of a filament channel. The pre-eruption force balance, consisting of an upward force due to the magnetic pressure of the sheared field balanced by a downward tension due to overlying un-sheared field, is widely believed to be disrupted by magnetic reconnection. Therefore, understanding initiation of solar explosive phenomena requires a true multi-scale model of reconnection onset driven by the buildup of magnetic shear. While the application of magnetic-field shear is a trivial matter in MHD simulations, it is a significant challenge in a PIC code. The driver must be implemented in a self-consistent manner and with boundary conditions that avoid the generation of waves that destroy the applied shear. In this work, we describe drivers for 2.5D, aperiodic, PIC systems and discuss the implementation of driver-consistent boundary conditions that allow a net electric current to flow through the walls. Preliminary tests of these boundaries with a MHD equilibrium are shown. This work was supported, in part, by the NASA Living With a Star TR&T Program.

  14. A Kinetic Approach to Shear Driven Magnetic Reconnection for Multi-Scale Modeling of CME Initiation

    NASA Astrophysics Data System (ADS)

    Black, Carrie; Antiochos, Spiro; DeVore, Rick; Germaschewski, Kai; Karpen, Judy

    2013-10-01

    In the standard model for coronal mass ejections (CME) and/or solar flares, the free energy for the event resides in the strongly sheared magnetic field of a filament channel. The pre-eruption force balance consisting of an upward force due to the magnetic pressure of the sheared field balanced by a downward tension due to overlying, un-sheared field is widely believed to be disrupted by magnetic reconnection. Therefore, understanding initiation of solar explosive phenomena requires a true multi-scale model of reconnection onset driven by the buildup of magnetic shear. While, the application of a magnetic field shear is a trivial matter in MHD simulations, it is significantly challenging to do so in a PIC code. The driver must be implemented in a self-consistent manner and with boundary conditions that avoid the generation of waves that destroy the applied shear. In this work, we describe such a driver for 2.5D, aperiodic, PIC system and discuss the implementation of driver consistent boundary conditions that allow a net electric current to flow through the walls. Preliminary tests of these boundaries with a MHD equilibrium are shown.

  15. A stochastic multi-scale model of electrical function in normal and depleted ICC networks.

    PubMed

    Gao, Jerry; Du, Peng; Archer, Rosalind; O'Grady, Greg; Gibbons, Simon J; Farrugia, Gianrico; Cheng, Leo K; Pullan, Andrew J

    2011-12-01

    Multi-scale modeling has become a productive strategy for quantifying interstitial cells of Cajal (ICC) network structure-function relationships, but the lack of large-scale ICC network imaging data currently limits modeling progress. The single normal equation simulation (SNESIM) algorithm was utilized to generate realistic virtual images of small real wild-type (WT) and 5-HT(2B)-receptor knockout (Htr2b(-/-)) mice ICC networks. Two metrics were developed to validate the performance of the algorithm: 1) network density, which is the proportion of ICC in the tissue; and 2) connectivity, which reflects the degree of connectivity of the ICC network. Following validation, the SNESIM algorithm was modified to allow variation in the degree of ICC network depletion. ICC networks from a range of depletion severities were generated, and the electrical activity over these networks was simulated. The virtual ICC networks generated by the original SNESIM algorithm were similar to that of their real counterparts. The electrical activity simulations showed that the maximum current density magnitude increased as the network density increased. In conclusion, the SNESIM algorithm is an effective tool for generating realistic virtual ICC networks. The modified SNESIM algorithm can be used with simulation techniques to quantify the physiological consequences of ICC network depletion at various physical scales.

  16. Realistic Modeling of Multi-Scale MHD Dynamics of the Solar Atmosphere

    NASA Technical Reports Server (NTRS)

    Kitiashvili, Irina; Mansour, Nagi N.; Wray, Alan; Couvidat, Sebastian; Yoon, Seokkwan; Kosovichev, Alexander

    2014-01-01

    Realistic 3D radiative MHD simulations open new perspectives for understanding the turbulent dynamics of the solar surface, its coupling to the atmosphere, and the physical mechanisms of generation and transport of non-thermal energy. Traditionally, plasma eruptions and wave phenomena in the solar atmosphere are modeled by prescribing artificial driving mechanisms using magnetic or gas pressure forces that might arise from magnetic field emergence or reconnection instabilities. In contrast, our 'ab initio' simulations provide a realistic description of solar dynamics naturally driven by solar energy flow. By simulating the upper convection zone and the solar atmosphere, we can investigate in detail the physical processes of turbulent magnetoconvection, generation and amplification of magnetic fields, excitation of MHD waves, and plasma eruptions. We present recent simulation results of the multi-scale dynamics of quiet-Sun regions, and energetic effects in the atmosphere and compare with observations. For the comparisons we calculate synthetic spectro-polarimetric data to model observational data of SDO, Hinode, and New Solar Telescope.

  17. Advanced Integration in Multi-Scale Mechanics and Welding Process Simulation in Weld Integrity Assessment

    SciTech Connect

    Vitek, J.M.; Wilkowski, G.M.; Brust, F.W.; Babu, S.

    2008-01-30

    In this project, mathematical models that predict the microstructure in pipeline steel welds were to be developed. These models were to be integrated with thermal models that describe the time-temperature history in the weld as a function of location in order to derive the spatial variation of microstructure in the weld. The microstructure predictions were also to be combined with microstructure-hardness relations, based on the additivity principle, to determine the spatial variation of hardness in the weld. EMC2 also developed microstructural models based on empirical relationships. ORNL was to pursue the development of more fundamental, theoretically based models. ORNL applied a previously developed model for inclusion formation to predict the extent and nature of inclusions that form during weld cooling from the liquid. This inclusion model was directly integrated with computational thermodynamics capability. A convenient user interface was developed for both the inclusion model and the thermodynamic phase-stability calculations. The microstructure model was based on the simultaneous transformation theory analysis as applied to the transformation of austenite to various ferrite constituents during weld cooling. The model available on the Materials Algorithm Project web site was used. Extensive modification of this model was required to correct problems with compilation and calculations as a function of the computational platform (Unix, Linux, Windows, etc.) that was used. The user interface for the inclusion model and thermodynamic phase-stability calculations was delivered to EMC2 along with the modified and correct microstructure model. Evaluation of the theoretically based model will be carried out and the predictions will be compared with experimental results as well as predictions based on the empirical models developed by EMC2.

  18. Multi-scale modelling of strongly heterogeneous 3D composite structures using spatial Voronoi tessellation

    NASA Astrophysics Data System (ADS)

    El Said, Bassam; Ivanov, Dmitry; Long, Andrew C.; Hallett, Stephen R.

    2016-03-01

    3D composite materials are characterized by complex internal yarn architectures, leading to complex deformation and failure development mechanisms. Net-shaped preforms, which are originally periodic in nature, lose their periodicity when the fabric is draped, deformed on a tool, and consolidated to create geometrically complex composite components. As a result, the internal yarn architecture, which dominates the mechanical behaviour, becomes dependent on the structural geometry. Hence, predicting the mechanical behaviour of 3D composites requires an accurate representation of the yarn architecture within structural scale models. When applied to 3D composites, conventional finite element modelling techniques are limited to either homogenised properties at the structural scale, or the unit cell scale for a more detailed material property definition. Consequently, these models fail to capture the complex phenomena occurring across multiple length scales and their effects on a 3D composite's mechanical response. Here a multi-scale modelling approach based on a 3D spatial Voronoi tessellation is proposed. The model creates an intermediate length scale suitable for homogenisation to deal with the non-periodic nature of the final material. Information is passed between the different length scales to allow for the effect of the structural geometry to be taken into account on the smaller scales. The stiffness and surface strain predictions from the proposed model have been found to be in good agreement with experimental results. The proposed modelling framework has been used to gain important insight into the behaviour of this category of materials. It has been observed that the strain and stress distributions are strongly dependent on the internal yarn architecture and consequently on the final component geometry. Even for simple coupon tests, the internal architecture and geometric effects dominate the mechanical response. Consequently, the behaviour of 3D woven

  19. A Unified Multi-Scale Model for Pore-Scale Flow Simulations in Soils

    SciTech Connect

    Yang, Xiaofan; Liu, Chongxuan; Shang, Jianying; Fang, Yilin; Bailey, Vanessa L.

    2014-01-30

    Pore-scale simulations have received increasing interest in subsurface sciences to provide mechanistic insights into the macroscopic phenomena of water flow and reactive transport processes. The application of the pore scale simulations to soils and sediments is, however, challenged because of the characterization limitation that often only allows partial resolution of pore structure and geometry. A significant proportion of the pore space in soils and sediments is below the spatial resolution, forming a mixed media of pore and porous domains. Here we reported a unified multi-scale model (UMSM) that can be used to simulate water flow and transport in mixed media of pore and porous domains under both saturated and unsaturated conditions. The approach modifies the classic Navier-Stokes equation by adding a Darcy term to describe fluid momentum and uses a generalized mass balance equation for saturated and unsaturated conditions. By properly defining physical parameters, the UMSM can be applied in both pore and porous domains. This paper describes the set of equations for the UMSM, a series of validation cases under saturated or unsaturated conditions, and a real soil case for the application of the approach.

  20. using multi-scale measurements of pitch angle distribution to test magnetospheric relativistic electron energization models

    NASA Astrophysics Data System (ADS)

    Kanekal, S. G.; Friedel, R. H. W.; Reeves, E. G. D.

    Detailed investigation of pitch angle distributions during the course of a relativistic electron energization event can aid in identifying the dominant physical process underlying the event. Current models of electron energization employ a variety physical processes ranging from radial diffusion to in-situ acceleration mechanisms. These processes result in different pitch angle distributions of energized electrons, for example radial diffusion dominated events have a pancake-type distribution. We present the results of a statistical survey of multi-scale electron pitch angle measurements during relativistic electron events. Measurements of in-situ pitch angle evolution at geosynchronous altitude are combined with measurements of global isotropization time scales. We use data from energetic particle sensors onboard SAMPEX and pitch angle data from the SOPA and ESP sensors onboard LANL spacecraft. The LANL measurements provide a microscopic view of the electron pitch angle distribution. Combining electron flux measurements at geosynchronous altitudes with those measured by SAMPEX which is in low earth orbit provides a macroscopic global view of the flux isotropization.

  1. Predictive Maturity of Multi-Scale Simulation Models for Fuel Performance

    SciTech Connect

    Atamturktur, Sez; Unal, Cetin; Hemez, Francois; Williams, Brian; Tome, Carlos

    2015-03-16

    The project proposed to provide a Predictive Maturity Framework with its companion metrics that (1) introduce a formalized, quantitative means to communicate information between interested parties, (2) provide scientifically dependable means to claim completion of Validation and Uncertainty Quantification (VU) activities, and (3) guide the decision makers in the allocation of Nuclear Energy’s resources for code development and physical experiments. The project team proposed to develop this framework based on two complimentary criteria: (1) the extent of experimental evidence available for the calibration of simulation models and (2) the sophistication of the physics incorporated in simulation models. The proposed framework is capable of quantifying the interaction between the required number of physical experiments and degree of physics sophistication. The project team has developed this framework and implemented it with a multi-scale model for simulating creep of a core reactor cladding. The multi-scale model is composed of the viscoplastic self-consistent (VPSC) code at the meso-scale, which represents the visco-plastic behavior and changing properties of a highly anisotropic material and a Finite Element (FE) code at the macro-scale to represent the elastic behavior and apply the loading. The framework developed takes advantage of the transparency provided by partitioned analysis, where independent constituent codes are coupled in an iterative manner. This transparency allows model developers to better understand and remedy the source of biases and uncertainties, whether they stem from the constituents or the coupling interface by exploiting separate-effect experiments conducted within the constituent domain and integral-effect experiments conducted within the full-system domain. The project team has implemented this procedure with the multi- scale VPSC-FE model and demonstrated its ability to improve the predictive capability of the model. Within this

  2. Evaluation of the Multi-Scale Modeling Framework using Data from the Atmospheric Radiation Measurement Program

    SciTech Connect

    Ovchinnikov, Mikhail; Ackerman, Thomas P.; Marchand, Roger T.; Khairoutdinov, Marat

    2004-07-01

    One of the goals of the Atmospheric Radiation Measurement (ARM) program was to provide long-term observations for evaluation of cloud and radiation treatment in global climate models. Unfortunately, traditional parametric approach of diagnosing cloud and radiation properties from large-scale model fields is not well suited for comparison with observed time series at selected locations. A recently emerging approach called the multi-scale modeling framework (MMF) has shown promise to bridge the gap. MMF consists of a two-dimensional cloud system resolving model (CSRM) embedded into each CAM grid column of the Community Atmospheric Model (CAM), thereby computing cloud properties at a scale that is more consistent with observations. Because the approach is computationally expensive only limited simulations have been carried out. In this presentation, we will present a comparison of data from two ARM sites, one at the Southern Great Plains (SGP) in Oklahoma and one at Nauru island in the Tropical Western Pacific (TWP) region, with output from both CAM and MMF. Two sets of one year long simulations are considered: one using climatological sea surface temperatures (SST) and another using 1999 SST. Each set includes a run with MMF as well as CAM run with traditional or standard cloud and radiation treatment. Time series of cloud fraction, precipitation intensity, and downwelling solar radiation flux at the surface are statistically analyzed. For the TWP site, nearly all parameters of frequency distributions of these variables from MMF run are shown to be more consistent with observation than those from CAM run. For the SGP, the improvements are marginal.

  3. HYPERstream: a multi-scale framework for streamflow routing in large-scale hydrological model

    NASA Astrophysics Data System (ADS)

    Piccolroaz, Sebastiano; Di Lazzaro, Michele; Zarlenga, Antonio; Majone, Bruno; Bellin, Alberto; Fiori, Aldo

    2016-05-01

    We present HYPERstream, an innovative streamflow routing scheme based on the width function instantaneous unit hydrograph (WFIUH) theory, which is specifically designed to facilitate coupling with weather forecasting and climate models. The proposed routing scheme preserves geomorphological dispersion of the river network when dealing with horizontal hydrological fluxes, irrespective of the computational grid size inherited from the overlaying climate model providing the meteorological forcing. This is achieved by simulating routing within the river network through suitable transfer functions obtained by applying the WFIUH theory to the desired level of detail. The underlying principle is similar to the block-effective dispersion employed in groundwater hydrology, with the transfer functions used to represent the effect on streamflow of morphological heterogeneity at scales smaller than the computational grid. Transfer functions are constructed for each grid cell with respect to the nodes of the network where streamflow is simulated, by taking advantage of the detailed morphological information contained in the digital elevation model (DEM) of the zone of interest. These characteristics make HYPERstream well suited for multi-scale applications, ranging from catchment up to continental scale, and to investigate extreme events (e.g., floods) that require an accurate description of routing through the river network. The routing scheme enjoys parsimony in the adopted parametrization and computational efficiency, leading to a dramatic reduction of the computational effort with respect to full-gridded models at comparable level of accuracy. HYPERstream is designed with a simple and flexible modular structure that allows for the selection of any rainfall-runoff model to be coupled with the routing scheme and the choice of different hillslope processes to be represented, and it makes the framework particularly suitable to massive parallelization, customization according to

  4. Simulations of Ecosystem Hydrological Processes Using a Unified Multi-Scale Model

    SciTech Connect

    Yang, Xiaofan; Liu, Chongxuan; Fang, Yilin; Hinkle, Ross; Li, Hongyi; Bailey, Vanessa L.; Bond-Lamberty, Benjamin

    2015-01-24

    This paper presents a unified multi-scale model (UMSM) that we developed to simulate hydrological processes in an ecosystem containing both surface water and groundwater. The UMSM approach modifies the Navier–Stokes equation by adding a Darcy force term to formulate a single set of equations to describe fluid momentum and uses a generalized equation to describe fluid mass balance. The advantage of the approach is that the single set of the equations can describe hydrological processes in both surface water and groundwater where different models are traditionally required to simulate fluid flow. This feature of the UMSM significantly facilitates modelling of hydrological processes in ecosystems, especially at locations where soil/sediment may be frequently inundated and drained in response to precipitation, regional hydrological and climate changes. In this paper, the UMSM was benchmarked using WASH123D, a model commonly used for simulating coupled surface water and groundwater flow. Disney Wilderness Preserve (DWP) site at the Kissimmee, Florida, where active field monitoring and measurements are ongoing to understand hydrological and biogeochemical processes, was then used as an example to illustrate the UMSM modelling approach. The simulations results demonstrated that the DWP site is subject to the frequent changes in soil saturation, the geometry and volume of surface water bodies, and groundwater and surface water exchange. All the hydrological phenomena in surface water and groundwater components including inundation and draining, river bank flow, groundwater table change, soil saturation, hydrological interactions between groundwater and surface water, and the migration of surface water and groundwater interfaces can be simultaneously simulated using the UMSM. Overall, the UMSM offers a cross-scale approach that is particularly suitable to simulate coupled surface and ground water flow in ecosystems with strong surface water and groundwater interactions.

  5. Object-based class modelling for multi-scale riparian forest habitat mapping

    NASA Astrophysics Data System (ADS)

    Strasser, Thomas; Lang, Stefan

    2015-05-01

    Object-based class modelling allows for mapping complex, hierarchical habitat systems. The riparian zone, including forests, represents such a complex ecosystem. Forests within riparian zones are biologically high productive and characterized by a rich biodiversity; thus considered of high community interest with an imperative to be protected and regularly monitored. Satellite earth observation (EO) provides tools for capturing the current state of forest habitats such as forest composition including intermixture of non-native tree species. Here we present a semi-automated object based image analysis (OBIA) approach for the mapping of riparian forests by applying class modelling of habitats based on the European Nature Information System (EUNIS) habitat classifications and the European Habitats Directive (HabDir) Annex 1. A very high resolution (VHR) WorldView-2 satellite image provided the required spatial and spectral details for a multi-scale image segmentation and rule-base composition to generate a six-level hierarchical representation of riparian forest habitats. Thereby habitats were hierarchically represented within an image object hierarchy as forest stands, stands of homogenous tree species and single trees represented by sunlit tree crowns. 522 EUNIS level 3 (EUNIS-3) habitat patches with a mean patch size (MPS) of 12,349.64 m2 were modelled from 938 forest stand patches (MPS = 6868.20 m2) and 43,742 tree stand patches (MPS = 140.79 m2). The delineation quality of the modelled EUNIS-3 habitats (focal level) was quantitatively assessed to an expert-based visual interpretation showing a mean deviation of 11.71%.

  6. Multi-Scale Model of Galactic Cosmic Ray Effects on the Hippocampus

    NASA Astrophysics Data System (ADS)

    Cucinotta, Francis

    An important concern for risk assessment from galactic cosmic ray (GCR) exposures is impacts to the central nervous systems including changes in cognition, and associations with increased risk of Alzheimer’s disease (AD). AD, which affects about 50 percent of the population above age 80-yr, is a degenerative disease that worsens with time after initial onset leading to death, and has no known cure. AD is difficult to detect at early stages, and the small number of epidemiology studies that have considered the possibility have not identified an association with low dose radiation. However, experimental studies in transgenic mice suggest the possibility exits. We discuss modeling approaches to consider mechanisms whereby GCR would accelerate the occurrence of AD to earlier ages. Biomarkers of AD include Amyloid beta plaques, and neurofibrillary tangles (NFT) made up of aggregates of the hyper-phosphorylated form of the micro-tubule associated, tau protein. Related markers include synaptic degeneration, dendritic spine loss, and neuronal cell loss through apoptosis. GCR may affect these processes by causing oxidative stress, aberrant signaling following DNA damage, and chronic neuro-inflammation. Cell types considered in multi-scale models are neurons, astrocytes, and microglia. We developed biochemical and cell kinetics models of DNA damage signaling related to glycogen synthase kinase-3 beta and neuro-inflammation, and considered approaches to develop computer simulations of GCR induced cell interactions and their relationships to Amyloid beta plaques and NFTs. Comparison of model results to experimental data for the age specific development of plaques in transgenic mice and predictions of space radiation effects will be discussed.

  7. Multi-scale modeling of the human cardiovascular system with applications to aortic valvular and arterial stenoses.

    PubMed

    Liang, Fuyou; Takagi, Shu; Himeno, Ryutaro; Liu, Hao

    2009-07-01

    A computational model of the entire cardiovascular system is established based on multi-scale modeling, where the arterial tree is described by a one-dimensional model coupled with a lumped parameter description of the remainder. The resultant multi-scale model forms a closed loop, thus placing arterial wave propagation into a global hemodynamic environment. The model is applied to study the global hemodynamic influences of aortic valvular and arterial stenoses located in various regions. Obtained results show that the global hemodynamic influences of the stenoses depend strongly on their locations in the arterial system, particularly, the characteristics of hemodynamic changes induced by the aortic valvular and aortic stenoses are pronounced, which imply the possibility of noninvasively detecting the presence of the stenoses from peripheral pressure pulses. The variations in aortic pressure/flow pulses with the stenoses play testimony to the significance of modeling the entire cardiovascular system in the study of arterial diseases.

  8. A Nonlinear Multi-Scale Interaction Model for Atmospheric Blocking: The Eddy-Blocking Matching Mechanism

    NASA Astrophysics Data System (ADS)

    Luo, Dehai; Cha, Jing; Zhong, Linhao; Dai, Aiguo

    2014-05-01

    In this paper, a nonlinear multi-scale interaction (NMI) model is used to propose an eddy-blocking matching (EBM) mechanism to account for how synoptic eddies reinforce or suppress a blocking flow. It is shown that the spatial structure of the eddy vorticity forcing (EVF) arising from upstream synoptic eddies determines whether an incipient block can grow into a meandering blocking flow through its interaction with the transient synoptic eddies from the west. Under certain conditions, the EVF exhibits a low-frequency oscillation on timescales of 2-3 weeks. During the EVF phase with a negative-over- positive dipole structure, a blocking event can be resonantly excited through the transport of eddy energy into the incipient block by the EVF. As the EVF changes into an opposite phase, the blocking decays. The NMI model produces life cycles of blocking events that resemble observations. Moreover, it is shown that the eddy north-south straining is a response of the eddies to a dipole- or Ω-type block. In our model, as in observations, two synoptic anticyclones (cyclones) can attract and merge with one another as the blocking intensifies, but only when the feedback of the blocking on the eddies is included. Thus, we attribute the eddy straining and associated vortex interaction to the feedback of the intensified blocking on synoptic eddies. The results illustrate the concomitant nature of the eddy deformation, whose role as a PV source for the blocking flow becomes important only during the mature stage of a block. Our EBM mechanism suggests that an incipient block flow is amplified (or suppressed) under certain conditions by the EVF coming from the upstream of the blocking region.

  9. The NCEP Eulerian Non-hydrostatic Multi-scale Model (NMMB)

    NASA Astrophysics Data System (ADS)

    Janjic, Zavisa; Vasic, Ratko; Jovic, Dusan; Black, Tom

    2014-05-01

    The development of the unified Non-hydrostatic Multi-scale Model (NMMB) has continued at NCEP. The model dynamics preserve a number of important properties of differential operators and conserve a variety of first order and quadratic quantities. The nonlinear dynamics is controlled by conserving energy and enstrophy in case of non-divergent flow. Over-specification of vertical velocity is avoided. The physical package was developed from the WRF NMM's physics, but other physics options are also available. The regional version of the NMMB is run operationally as the main deterministic North American short-range forecasting model (NAM) and in a number of other applications. The global NMMB also has been run over the last few years experimentally in order to assess its capabilities and develop it further. In terms of large scale metrics, the performance of the global NMMB in medium range weather forecasting has been generally comparable to that of other major medium range forecasting systems. Its computational efficiency satisfies and exceeds the current and projected operational requirements. Recently, the transition has started of the operational hurricane forecasting system HWRF from the WRF NMM dynamics to those of the NMMB. This system involves the use of a hierarchy of 2-way interactive telescoping moving nests. The work on the interaction between clouds and radiation has continued. Extended range forecasts showed large sensitivity to the method for representing clouds. With the clouds represented by optical properties of their microphysics species, the results depend on the microphysics scheme used. Taking into account the impact of convective clouds remains a challenge with this approach. Development of an indigenous data assimilation system for the global NMMB has commenced. The system is based on the hybrid ensemble Kalman filter/3DVAR technique. It is believed that the potential of the NMMB can be better assessed using its own dedicated data assimilation

  10. A switching multi-scale dynamical network model of EEG/MEG.

    PubMed

    Olier, Iván; Trujillo-Barreto, Nelson J; El-Deredy, Wael

    2013-12-01

    We introduce a new generative model of the Encephalography (EEG/MEG) data, the inversion of which allows for inferring the locations and temporal evolution of the underlying sources as well as their dynamical interactions. The proposed Switching Mesostate Space Model (SMSM) builds on the multi-scale generative model for EEG/MEG by Daunizeau and Friston (2007). SMSM inherits the assumptions that (1) bioelectromagnetic activity is generated by a set of distributed sources, (2) the dynamics of these sources can be modelled as random fluctuations about a small number of mesostates, and (3) the number of mesostates engaged by a cognitive task is small. Additionally, four generalising assumptions are now included: (4) the mesostates interact according to a full Dynamical Causal Network (DCN) that can be estimated; (5) the dynamics of the mesostates can switch between multiple approximately linear operating regimes; (6) each operating regime remains stable over finite periods of time (temporal clusters); and (7) the total number of times the mesostates' dynamics can switch is small. The proposed model adds, therefore, a level of flexibility by accommodating complex brain processes that cannot be characterised by purely linear and stationary Gaussian dynamics. Importantly, the SMSM furnishes a new interpretation of the EEG/MEG data in which the source activity may have multiple discrete modes of behaviour, each with approximately linear dynamics. This is modelled by assuming that the connection strengths of the underlying mesoscopic DCN are time-dependent but piecewise constant, i.e. they can undergo discrete changes over time. A Variational Bayes inversion scheme is derived to estimate all the parameters of the model by maximising a (Negative Free Energy) lower bound on the model evidence. This bound is used to select among different model choices that are defined by the number of mesostates as well as by the number of stationary linear regimes. The full model is compared

  11. Structural optimization of composites using a multi-scale, hierarchical model

    NASA Astrophysics Data System (ADS)

    Kedlaya, Diwakar N.

    reinforced structure. Along with the above experiments, macro experiments are also carried out enabling and strengthening the UC and ISV model. New and improvised Genetic algorithm (GA) with markov model is developed and tested for structural optimization, to accommodate probabilistic UC stacking, variable initial population, variable community search, etc. Developed optimization tool enables suggest a particular shape, structure, material and architecture of the reinforced composite for a certain loading condition. This GA makes use of history, probability and memory alongside being a multi-objective, multi-constrained, multi-scaled global optimization technique. Critical scenario of airfoil and wing structure design and optimization is addressed in both static and dynamic cases. This opens up areas of prediction and design in dynamic loading conditions, especially in fields such as crashworthiness in cars, design of structure under aerodynamic loads etc.

  12. Multi-scale modeling of the structure and dynamics of macromolecules

    NASA Astrophysics Data System (ADS)

    Serohijos, Adrian Wendil R.

    Biology is defined by phenomena that are inherently complex spanning multiple length and time scales. To understand these processes, there is a need for multi-scale approaches that provide a coherent framework for describing and interrogating these phenomena. Here, we employ multiple approaches to investigate specific biological systems. The first system we studied was the cytoplasmic dynein motor, a protein that walks along the microtubule tracks in cells. The major objective in the dynein motors field is to understand its mechanism. Specifically, what is dynein's structure and how does it transduce chemical energy into mechanical work? We proposed a theoretical structural model of the motor and performed normal mode analysis and molecular dynamics on the motor unit structure. These studies hypothesized new structural features in the dynein motor unit and proposed a potential mechanism for energy transduction [5,6,80]. The second system we studied was the CFTR channel, which regulates ion transport in the apical membrane of epithelial cells. Mutations in the CFTR protein are the basis of the cystic fibosis disease. One of the primary question is how a single residue deletion (Phe508) lead to ˜90% of cystic fibrosis cases. We performed molecular dynamics simulation of the first nucleotide-binding domain of CFTR and showed that the wild type and mutant exhibit a difference in their folding kinetics, in agreement with experiments. These simulations also determined the potential structural origin of this misfolding defect. We also proposed a complete model of the CFTR channel to identify the location of the Phe508 residue in the whole protein. This result is important in understanding another aspect of the DeltaF508 defect, which is the misassembly of the whole CFTR protein during its biosynthesis.

  13. ADVANCED INTEGRATION OF MULTI-SCALE MECHANICS AND WELDING PROCESS SIMULATION IN WELD INTEGRITY ASSESSMENT

    SciTech Connect

    Wilkowski, Gery M.; Rudland, David L.; Shim, Do-Jun; Brust, Frederick W.; Babu, Sundarsanam

    2008-06-30

    The potential to save trillions of BTU’s in energy usage and billions of dollars in cost on an annual basis based on use of higher strength steel in major oil and gas transmission pipeline construction is a compelling opportunity recognized by both the US Department of Energy (DOE). The use of high-strength steels (X100) is expected to result in energy savings across the spectrum, from manufacturing the pipe to transportation and fabrication, including welding of line pipe. Elementary examples of energy savings include more the 25 trillion BTUs saved annually based on lower energy costs to produce the thinner-walled high-strength steel pipe, with the potential for the US part of the Alaskan pipeline alone saving more than 7 trillion BTU in production and much more in transportation and assembling. Annual production, maintenance and installation of just US domestic transmission pipeline is likely to save 5 to 10 times this amount based on current planned and anticipated expansions of oil and gas lines in North America. Among the most important conclusions from these studies were: • While computational weld models to predict residual stress and distortions are well-established and accurate, related microstructure models need improvement. • Fracture Initiation Transition Temperature (FITT) Master Curve properly predicts surface-cracked pipe brittle-to-ductile initiation temperature. It has value in developing Codes and Standards to better correlate full-scale behavior from either CTOD or Charpy test results with the proper temperature shifts from the FITT master curve method. • For stress-based flaw evaluation criteria, the new circumferentially cracked pipe limit-load solution in the 2007 API 1104 Appendix A approach is overly conservative by a factor of 4/π, which has additional implications. . • For strain-based design of girth weld defects, the hoop stress effect is the most significant parameter impacting CTOD-driving force and can increase the crack

  14. Multi-scale finite element modeling of strain localization in geomaterials with strong discontinuity

    NASA Astrophysics Data System (ADS)

    Lai, Timothy Yu

    2002-01-01

    Geomaterials such as soils and rocks undergo strain localization during various loading conditions. Strain localization manifests itself in the form of a shear band, a narrow zone of intense straining. It is now generally recognized that these localized deformations lead to an accelerated softening response and influence the response of structures at or near failure. In order to accurately predict the behavior of geotechnical structures, the effects of strain localization must be included in any model developed. In this thesis, a multi-scale Finite Element (FE) model has been developed that captures the macro- and micro-field deformation patterns present during strain localization. The FE model uses a strong discontinuity approach where a jump in the displacement field is assumed. The onset of strain localization is detected using bifurcation theory that checks when the governing equations lose ellipticity. Two types of bifurcation, continuous and discontinuous are considered. Precise conditions for plane strain loading conditions are reported for each type of bifurcation. Post-localization behavior is governed by the traction relations on the band. Different plasticity models such as Mohr-Coulomb, Drucker-Prager and a Modified Mohr-Coulomb yield were implemented together with cohesion softening and cutoff for the post-localization behavior. The FE model is implemented into a FORTRAN code SPIN2D-LOC using enhanced constant strain triangular (CST) elements. The model is formulated using standard Galerkin finite element method, applicable to problems under undrained conditions and small deformation theory. A band-tracing algorithm is implemented to track the propagation of the shear band. To validate the model, several simulations are performed from simple compression test of soft rock to simulation of a full-scale geosynthetic reinforced soil wall model undergoing strain localization. Results from both standard and enhanced FE method are included for comparison. The

  15. Seamless continental-domain hydrologic model parameter estimations with Multi-Scale Parameter Regionalization

    NASA Astrophysics Data System (ADS)

    Mizukami, Naoki; Clark, Martyn; Newman, Andrew; Wood, Andy

    2016-04-01

    Estimation of spatially distributed parameters is one of the biggest challenges in hydrologic modeling over a large spatial domain. This problem arises from methodological challenges such as the transfer of calibrated parameters to ungauged locations. Consequently, many current large scale hydrologic assessments rely on spatially inconsistent parameter fields showing patchwork patterns resulting from individual basin calibration or spatially constant parameters resulting from the adoption of default or a-priori estimates. In this study we apply the Multi-scale Parameter Regionalization (MPR) framework (Samaniego et al., 2010) to generate spatially continuous and optimized parameter fields for the Variable Infiltration Capacity (VIC) model over the contiguous United States(CONUS). The MPR method uses transfer functions that relate geophysical attributes (e.g., soil) to model parameters (e.g., parameters that describe the storage and transmission of water) at the native resolution of the geophysical attribute data and then scale to the model spatial resolution with several scaling functions, e.g., arithmetic mean, harmonic mean, and geometric mean. Model parameter adjustments are made by calibrating the parameters of the transfer function rather than the model parameters themselves. In this presentation, we first discuss conceptual challenges in a "model agnostic" continental-domain application of the MPR approach. We describe development of transfer functions for the soil parameters, and discuss challenges associated with extending MPR for VIC to multiple models. Next, we discuss the "computational shortcut" of headwater basin calibration where we estimate the parameters for only 500 headwater basins rather than conducting simulations for every grid box across the entire domain. We first performed individual basin calibration to obtain a benchmark of the maximum achievable performance in each basin, and examined their transferability to the other basins. We then

  16. A Comparison of Transfer Hamiltonian vs. DFT Methods in QM/CM Multi-Scale Modeling

    NASA Astrophysics Data System (ADS)

    Mallik, Aditi; Runge, Keith; Cheng, Hai-Ping; Dufty, James

    2004-11-01

    A method for a consistent embedding of a quantum (QM) domain in its classical (CM) environment has been developed for application in QM/CM simulations for multi-scale modeling. A benchmark system is considered: a silica nanorod in which a part of the rod is treated quantum mechanically and the rest is treated classically. This system is chosen because a full ab initio quantum data can be obtained for the entire rod to assess the quality of the proposed embedding technique. However, even at the quantum level each possible choice for the ab initio method entails approximations used to optimize the accuracy and speed of the calculations. Each approximation has its own advantages and limitations, but the embedding scheme should be insensitive to these. In order to test how robust our proposed embedding scheme is, we have chosen two different methods for the underlying quantum mechanical description. The first method used is the Transfer Hamiltonian (TH) Neglect of Diatomic Differential Overlap (NDDO) (Bartlett, 2003). The TH method uses a semi empirical Hamiltonian that has been parameterized to yield coupled cluster quality forces, thereby taking electron correlations into account like post-Hartree Fock methods. The second method used is the Born-Oppenheimer local spin density (Barnett and Landman, 1993) within density functional theory (DFT) and generalized gradient approximation (GGA). We use the Perdew-Burke-Ernzerhof (PBE) exchange correlation functional. Here, the embedding method and resulting QM/CM composite rods using the two different ab initio methods are compared for the silica nanorod. It is found that the two quantum rods have noticeable differences, although the embedding method for the equilibrium composite rods is faithful to the underlying quantum method in each case. Nonequilibrium elastic properties are discussed briefly.

  17. Multi-scale Rule-of-Mixtures Model of Carbon Nanotube/Carbon Fiber/Epoxy Lamina

    NASA Technical Reports Server (NTRS)

    Frankland, Sarah-Jane V.; Roddick, Jaret C.; Gates, Thomas S.

    2005-01-01

    A unidirectional carbon fiber/epoxy lamina in which the carbon fibers are coated with single-walled carbon nanotubes is modeled with a multi-scale method, the atomistically informed rule-of-mixtures. This multi-scale model is designed to include the effect of the carbon nanotubes on the constitutive properties of the lamina. It included concepts from the molecular dynamics/equivalent continuum methods, micromechanics, and the strength of materials. Within the model both the nanotube volume fraction and nanotube distribution were varied. It was found that for a lamina with 60% carbon fiber volume fraction, the Young's modulus in the fiber direction varied with changes in the nanotube distribution, from 138.8 to 140 GPa with nanotube volume fractions ranging from 0.0001 to 0.0125. The presence of nanotube near the surface of the carbon fiber is therefore expected to have a small, but positive, effect on the constitutive properties of the lamina.

  18. Selective ensemble modeling load parameters of ball mill based on multi-scale frequency spectral features and sphere criterion

    NASA Astrophysics Data System (ADS)

    Tang, Jian; Yu, Wen; Chai, Tianyou; Liu, Zhuo; Zhou, Xiaojie

    2016-01-01

    It is difficult to model multi-frequency signal, such as mechanical vibration and acoustic signals of wet ball mill in the mineral grinding process. In this paper, these signals are decomposed into multi-scale intrinsic mode functions (IMFs) by the empirical mode decomposition (EMD) technique. A new adaptive multi-scale spectral features selection approach based on sphere criterion (SC) is applied to these IMFs frequency spectra. The candidate sub-models are constructed by the partial least squares (PLS) with the selected features. Finally, the branch and bound based selective ensemble (BBSEN) algorithm is applied to select and combine these ensemble sub-models. This method can be easily extended to regression and classification problems with multi-time scale signal. We successfully apply this approach to a laboratory-scale ball mill. The shell vibration and acoustic signals are used to model mill load parameters. The experimental results demonstrate that this novel approach is more effective than the other modeling methods based on multi-scale frequency spectral features.

  19. Simulations of Tornadoes, Tropical Cyclones, MJOs, and QBOs, using GFDL's multi-scale global climate modeling system

    NASA Astrophysics Data System (ADS)

    Lin, Shian-Jiann; Harris, Lucas; Chen, Jan-Huey; Zhao, Ming

    2014-05-01

    A multi-scale High-Resolution Atmosphere Model (HiRAM) is being developed at NOAA/Geophysical Fluid Dynamics Laboratory. The model's dynamical framework is the non-hydrostatic extension of the vertically Lagrangian finite-volume dynamical core (Lin 2004, Monthly Wea. Rev.) constructed on a stretchable (via Schmidt transformation) cubed-sphere grid. Physical parametrizations originally designed for IPCC-type climate predictions are in the process of being modified and made more "scale-aware", in an effort to make the model suitable for multi-scale weather-climate applications, with horizontal resolution ranging from 1 km (near the target high-resolution region) to as low as 400 km (near the antipodal point). One of the main goals of this development is to enable simulation of high impact weather phenomena (such as tornadoes, thunderstorms, category-5 hurricanes) within an IPCC-class climate modeling system previously thought impossible. We will present preliminary results, covering a very wide spectrum of temporal-spatial scales, ranging from simulation of tornado genesis (hours), Madden-Julian Oscillations (intra-seasonal), topical cyclones (seasonal), to Quasi Biennial Oscillations (intra-decadal), using the same global multi-scale modeling system.

  20. Evaluating Goddard Multi-Scale Modeling Framework at Different fv-GCM Grid Spacing

    NASA Astrophysics Data System (ADS)

    Chern, J.; Matsui, T.; Shen, B.; Tao, W.

    2009-12-01

    The Goddard Multi-scale Modeling Framework (MMF) is based on the coupling of the two-dimensional Goddard Cumulus Ensemble (GCE) model and the finite-volume GCM (fv-GCM). Thus MMF enables explicit resolution of stochastic moist convection process by embedded GCE simulations, unlike traditional GCMs that rely on convection parameterization. At each fv-GCM column, the fv-GCM provides mean atmospheric conditions and large-scale temperature and moisture advection to drive the 2D GCE models, which feedback the tendencies of thermodynamic parameter and cloud statistics to the fv-GCM. Earlier investigations show that the Goddard MMF simulates better cloudiness (high and low), single ITCZ and a more realistic diurnal variation of rainfall than traditional GCMs. Another advantages of using the Goddard MMF is that the resolution of GCE-simulated clouds is compatible to satellite observations, while traditional GCM requires disaggregation of grid-volume feature to compare with high-resolution satellite observations. Thus, satellite instrumental simulator can be directly applied to translate MMF simulations into the satellite instrumental signals in straightforward way. In this year, we examine the sensitivity of the Goddard MMF simulation at different fv-GCM grid spacing, and evaluated performances against the TRMM satellite. Previously, fv-GCM was run at 2x2.5 degree horizontal lat-lon grid spacing, and we are currently running fv-GCM at 1x1.25 degree. We examine the performance of the Goddard MMF at different fv-GCM grid spacing with respect to rainfall frequency, rain structure, and microphysics using multi-sensor radiance-based evaluation method, known as the TRMM Triple-Sensor Three-step Evaluation Framework (T3EF). T3EF utilizes multi-sensor satellite simulators, Goddard Satellite Data Simulation Unit, and novel statistics of multi-sensor radiance and backscattering signals observed from the TRMM satellite. Specifically, T3EF compares GCE and satellite observations in

  1. Multi-scale Modeling of Power Plant Plume Emissions and Comparisons with Observations

    NASA Astrophysics Data System (ADS)

    Costigan, K. R.; Lee, S.; Reisner, J.; Dubey, M. K.; Love, S. P.; Henderson, B. G.; Chylek, P.

    2011-12-01

    The Remote Sensing Verification Project (RSVP) test-bed located in the Four Corners region of Arizona, Utah, Colorado, and New Mexico offers a unique opportunity to develop new approaches for estimating emissions of CO2. Two major power plants located in this area produce very large signals of co-emitted CO2 and NO2 in this rural region. In addition to the Environmental Protection Agency (EPA) maintaining Continuous Emissions Monitoring Systems (CEMS) on each of the power plant stacks, the RSVP program has deployed an array of in-situ and remote sensing instruments, which provide both point and integrated measurements. To aid in the synthesis and interpretation of the measurements, a multi-scale atmospheric modeling approach is implemented, using two atmospheric numerical models: the Weather Research and Forecasting Model with chemistry (WRF-Chem; Grell et al., 2005) and the HIGRAD model (Reisner et al., 2003). The high fidelity HIGRAD model incorporates a multi-phase Lagrangian particle based approach to track individual chemical species of stack plumes at ultra-high resolution, using an adaptive mesh. It is particularly suited to model buoyancy effects and entrainment processes at the edges of the power plant plumes. WRF-Chem is a community model that has been applied to a number of air quality problems and offers several physical and chemical schemes that can be used to model the transport and chemical transformation of the anthropogenic plumes out of the local region. Multiple nested grids employed in this study allow the model to incorporate atmospheric variability ranging from synoptic scales to micro-scales (~200 m), while including locally developed flows influenced by the nearby complex terrain of the San Juan Mountains. The simulated local atmospheric dynamics are provided to force the HIGRAD model, which links mesoscale atmospheric variability to the small-scale simulation of the power plant plumes. We will discuss how these two models are applied and

  2. Multi-scale Model of Residual Strength of 2D Plain Weave C/SiC Composites in Oxidation Atmosphere

    NASA Astrophysics Data System (ADS)

    Chen, Xihui; Sun, Zhigang; Sun, Jianfen; Song, Yingdong

    2016-06-01

    Multi-scale models play an important role in capturing the nonlinear response of woven carbon fiber reinforced ceramic matrix composites. In plain weave carbon fiber/silicon carbon (C/SiC) composites, the carbon fibers and interphases will be oxidized at elevated temperature and the strength of the composite will be degraded when oxygen enters micro-cracks formed in the as-produced parts due to the mismatch in thermal properties between constituents. As a result of the oxidation on fiber surface, fiber shows a notch-like morphology. In this paper, the change rule of fiber notch depth is fitted by circular function. And a multi-scale model based upon the change rule of fiber notch depth is developed to simulate the residual strength and post-oxidation stress-strain curves of the composite. The multi-scale model is able to accurately predict the residual strength and post-oxidation stress-strain curves of the composite. Besides, the simulated residual strength and post-oxidation stress-strain curves of 2D plain weave C/SiC composites in oxidation atmosphere show good agreements with experimental results. Furthermore, the oxidation time and temperature of the composite are investigated to show their influences upon the residual strength and post-oxidation stress-strain curves of plain weave C/SiC composites.

  3. Multi-scale simulation method with coupled finite/discrete element model and its application

    NASA Astrophysics Data System (ADS)

    Fang, Xiwu; Liu, Zhenyu; Tan, Jianrong; Qiu, Chan; Chen, Fengbei

    2013-07-01

    The existing research on continuous structure is usually analyzed with finite element method (FEM) and granular medium with discrete element method (DEM), but there are few researches on the coupling interaction between continuous structure and discrete medium. To the issue of this coupling interaction, a multi-scale simulation method with coupled finite/discrete element model is put forward, in their respective domains of discrete and finite elements, the nodes follow force law and motion law of their own method, and on the their interaction interface, the touch type between discrete and finite elements is distinguished as two types: full touch and partial touch, the interaction force between them is calculated with linear elastic model. For full touch, the contact force is proportional to the overlap distance between discrete element and finite element patch. For partial touch, first the finite element patch is extended on all sides indefinitely to be a complete plane, the full contact force can be obtained with the touch type between discrete element and plane being viewed as full touch, then the full overlap area between them and the actual overlap area between discrete element and finite element patch are computed, the actual contact force is obtained by scaling the full contact force with a factor η which is determined by the ratio of the actual overlap area to the full overlap area. The contact force is equivalent to the finite element nodes and the force and displacement on the nodes can be computed, so the ideal simulation results can be got. This method has been used to simulate the cutter disk of the earth pressure balance shield machine (EPBSM) made in North Heavy Industry (NHI) with its excavation diameter of 6.28 m cutting and digging the sandy clay layer. The simulation results show that as the gradual increase of excavating depth of the cutter head, the maximum stress occurs at the roots of cutters on the cutter head, while for the soil, the

  4. Advancing a distributed multi-scale computing framework for large-scale high-throughput discovery in materials science.

    PubMed

    Knap, J; Spear, C E; Borodin, O; Leiter, K W

    2015-10-30

    We describe the development of a large-scale high-throughput application for discovery in materials science. Our point of departure is a computational framework for distributed multi-scale computation. We augment the original framework with a specialized module whose role is to route evaluation requests needed by the high-throughput application to a collection of available computational resources. We evaluate the feasibility and performance of the resulting high-throughput computational framework by carrying out a high-throughput study of battery solvents. Our results indicate that distributed multi-scale computing, by virtue of its adaptive nature, is particularly well-suited for building high-throughput applications.

  5. Use of ARM Data to address the Climate Change Further Development and Applications of A Multi-scale Modeling Framework

    SciTech Connect

    David A. Randall; Marat Khairoutdinov

    2007-12-14

    The Colorado State University (CSU) Multi-scale Modeling Framework (MMF) is a new type of general circulation model (GCM) that replaces the conventional parameterizations of convection, clouds and boundary layer with a cloud-resolving model (CRM) embedded into each grid column. The MMF that we have been working with is a “super-parameterized” version of the Community Atmosphere Model (CAM). As reported in the publications listed below, we have done extensive work with the model. We have explored the MMF’s performance in several studies, including an AMIP run and a CAPT test, and we have applied the MMF to an analysis of climate sensitivity.

  6. Comparison of single- and multi-scale models for the prediction of the Culicoides biting midge distribution in Germany.

    PubMed

    Lühken, Renke; Gethmann, Jörn Martin; Kranz, Petra; Steffenhagen, Pia; Staubach, Christoph; Conraths, Franz J; Kiel, Ellen

    2016-01-01

    This study analysed Culicoides presence-absence data from 46 sampling sites in Germany, where monitoring was carried out from April 2007 until May 2008. Culicoides presence-absence data were analysed in relation to land cover data, in order to study whether the prevalence of biting midges is correlated to land cover data with respect to the trapping sites. We differentiated eight scales, i.e. buffer zones with radii of 0.5, 1, 2, 3, 4, 5, 7.5 and 10 km, around each site, and chose several land cover variables. For each species, we built eight single-scale models (i.e. predictor variables from one of the eight scales for each model) based on averaged, generalised linear models and two multiscale models (i.e. predictor variables from all of the eight scales) based on averaged, generalised linear models and generalised linear models with random forest variable selection. There were no significant differences between performance indicators of models built with land cover data from different buffer zones around the trapping sites. However, the overall performance of multi-scale models was higher than the alternatives. Furthermore, these models mostly achieved the best performance for the different species using the index area under the receiver operating characteristic curve. However, as also presented in this study, the relevance of the different variables could significantly differ between various scales, including the number of species affected and the positive or negative direction. This is an even more severe problem if multi-scale models are concerned, in which one model can have the same variable at different scales but with different directions, i.e. negative and positive direction of the same variable at different scales. However, multi-scale modelling is a promising approach to model the distribution of Culicoides species, accounting much more for the ecology of biting midges, which uses different resources (breeding sites, hosts, etc.) at different scales

  7. Multi-scale through-process modeling and simulation in precision forming of complex components of difficult-to-deform material

    NASA Astrophysics Data System (ADS)

    Yang, H.; Fan, X. G.; Li, H. W.; Li, H.; Zhan, M.; Sun, Z. C.; Guo, L. G.; Liu, Y. L.

    2013-05-01

    Precision forming of complex components of difficult-to-deform material, which satisfies the increasing demands of high performance and light weight in aerospace industries, has become a research frontier in advanced plastic forming domains. Owning to the usage of difficult-to-deform materials and hard-to-form complex structure, and the requirement of excellent service performance, significant unequal deformation takes place during plastic forming of such components, which would increase the forming load, produce forming defects, deteriorate the service performance and make the control and optimization of the forming process difficult. How to coordinate and control the unequal deformation is the key problem urgently to be solved. The through-process multi-scale modeling and simulation are essential for developing control method of unequal deformation. To this end, a through-process multi-scale modeling strategy was proposed in the present work. It is composed of a microscale cellular automaton model which predicts the microstructural morphology development, a mesoscale crystal plasticity model which characterizes the mechanism of unequal deformation, a coupled macro-microscale internal state variable model which predicts the constitutive behavior and microstructure evolution of the material, and a macroscale finite element model which predicts the forming regulations and defects. The strategy was applied to the isothermal local loading forming of large-scale complex titanium alloy component. The obtained results can guide the integrated forming of shape and performance in manufacturing complex components of difficult-to-deform material.

  8. Overview of Computer-Aided Engineering of Batteries and Introduction to Multi-Scale, Multi-Dimensional Modeling of Li-Ion Batteries (Presentation)

    SciTech Connect

    Pesaran, A.; Kim, G. H.; Smith, K.; Santhanagopalan, S.; Lee, K. J.

    2012-05-01

    This 2012 Annual Merit Review presentation gives an overview of the Computer-Aided Engineering of Batteries (CAEBAT) project and introduces the Multi-Scale, Multi-Dimensional model for modeling lithium-ion batteries for electric vehicles.

  9. Multi-scale renormalization

    NASA Astrophysics Data System (ADS)

    Ford, C.; Wiesendanger, C.

    1997-02-01

    The standard MS renormalization prescription is inadequate for dealing with multi-scale problems. To illustrate this we consider the computation of the effective potential in the Higgs-Yukawa model. It is argued that it is natural to employ a two-scale renormalization group. We give a modified version of a two-scale scheme introduced by Einhorn and Jones. In such schemes the beta functions necessarily contain potentially large logarithms of the RG scale ratios. For credible perturbation theory one must implement a large logarithms resummation on the beta functions themselves. We show how the integrability condition for the two RG equations allows one to perform this resummation.

  10. Storm surge simulation along the U.S. East and Gulf Coasts using a multi-scale numerical model approach

    NASA Astrophysics Data System (ADS)

    Xu, Hongzhou; Zhang, Keqi; Shen, Jian; Li, Yuepeng

    2010-12-01

    The effectiveness of simulating surge inundation using the Eulerian-Lagrangian circulation (ELCIRC) model over multi-scale unstructured grids was examined in this study. The large domain model grid encompasses the western North Atlantic Ocean, the Gulf of Mexico, and the Caribbean Sea to appropriately account for remote and resonance effects during hurricane events and simplify the specification of the open boundary condition. The U.S. East and Gulf Coasts were divided into 12 overlapping basins with fine-resolution (up to 30 × 30 m) grids to model overland surge flooding. These overlapping basins have different fine-resolution grids near the coastal region, but have an identical coarse-resolution grid in the offshore region within the large model domain. Thus, the storm surge prediction can be conducted without reducing computation efficiency by executing multiple model runs with local fine-resolution grids where potential hurricane landfalls may occur. The capability of the multi-scale approach was examined by simulating storm surge caused by Hurricanes Andrew (1992) and Isabel (2003) along the South Florida coast and in the Chesapeake Bay. Comparisons between simulated and observed results suggest that multi-scale models proficiently simulated storm surges in the Biscayne Bay and the Chesapeake Bay during two hurricanes. A series of sensitivity tests demonstrated that the simulation of surge flooding was improved when LiDAR topographic data and special bottom drag coefficient values for mangrove forests were employed. The tests also showed that appropriate representation of linear hydrologic features is important for computing surge inundation in an urban area.

  11. Multi-scale modeling of microstructure dependent intergranular brittle fracture using a quantitative phase-field based method

    SciTech Connect

    Chakraborty, Pritam; Zhang, Yongfeng; Tonks, Michael R.

    2015-12-07

    In this study, the fracture behavior of brittle materials is strongly influenced by their underlying microstructure that needs explicit consideration for accurate prediction of fracture properties and the associated scatter. In this work, a hierarchical multi-scale approach is pursued to model microstructure sensitive brittle fracture. A quantitative phase-field based fracture model is utilized to capture the complex crack growth behavior in the microstructure and the related parameters are calibrated from lower length scale atomistic simulations instead of engineering scale experimental data. The workability of this approach is demonstrated by performing porosity dependent intergranular fracture simulations in UO2 and comparing the predictions with experiments.

  12. Modeling multi-scale aerosol dynamics and micro-environmental air quality near a large highway intersection using the CTAG model.

    PubMed

    Wang, Yan Jason; Nguyen, Monica T; Steffens, Jonathan T; Tong, Zheming; Wang, Yungang; Hopke, Philip K; Zhang, K Max

    2013-01-15

    A new methodology, referred to as the multi-scale structure, integrates "tailpipe-to-road" (i.e., on-road domain) and "road-to-ambient" (i.e., near-road domain) simulations to elucidate the environmental impacts of particulate emissions from traffic sources. The multi-scale structure is implemented in the CTAG model to 1) generate process-based on-road emission rates of ultrafine particles (UFPs) by explicitly simulating the effects of exhaust properties, traffic conditions, and meteorological conditions and 2) to characterize the impacts of traffic-related emissions on micro-environmental air quality near a highway intersection in Rochester, NY. The performance of CTAG, evaluated against with the field measurements, shows adequate agreement in capturing the dispersion of carbon monoxide (CO) and the number concentrations of UFPs in the near road micro-environment. As a proof-of-concept case study, we also apply CTAG to separate the relative impacts of the shutdown of a large coal-fired power plant (CFPP) and the adoption of the ultra-low-sulfur diesel (ULSD) on UFP concentrations in the intersection micro-environment. Although CTAG is still computationally expensive compared to the widely-used parameterized dispersion models, it has the potential to advance our capability to predict the impacts of UFP emissions and spatial/temporal variations of air pollutants in complex environments. Furthermore, for the on-road simulations, CTAG can serve as a process-based emission model; Combining the on-road and near-road simulations, CTAG becomes a "plume-in-grid" model for mobile emissions. The processed emission profiles can potentially improve regional air quality and climate predictions accordingly.

  13. Toward Multi-scale Modeling and simulation of conduction in heterogeneous materials

    SciTech Connect

    Lechman, Jeremy B.; Battaile, Corbett Chandler.; Bolintineanu, Dan; Cooper, Marcia A.; Erikson, William W.; Foiles, Stephen M.; Kay, Jeffrey J; Phinney, Leslie M.; Piekos, Edward S.; Specht, Paul Elliott; Wixom, Ryan R.; Yarrington, Cole

    2015-01-01

    This report summarizes a project in which the authors sought to develop and deploy: (i) experimental techniques to elucidate the complex, multiscale nature of thermal transport in particle-based materials; and (ii) modeling approaches to address current challenges in predicting performance variability of materials (e.g., identifying and characterizing physical- chemical processes and their couplings across multiple length and time scales, modeling information transfer between scales, and statically and dynamically resolving material structure and its evolution during manufacturing and device performance). Experimentally, several capabilities were successfully advanced. As discussed in Chapter 2 a flash diffusivity capability for measuring homogeneous thermal conductivity of pyrotechnic powders (and beyond) was advanced; leading to enhanced characterization of pyrotechnic materials and properties impacting component development. Chapter 4 describes success for the first time, although preliminary, in resolving thermal fields at speeds and spatial scales relevant to energetic components. Chapter 7 summarizes the first ever (as far as the authors know) application of TDTR to actual pyrotechnic materials. This is the first attempt to actually characterize these materials at the interfacial scale. On the modeling side, new capabilities in image processing of experimental microstructures and direct numerical simulation on complicated structures were advanced (see Chapters 3 and 5). In addition, modeling work described in Chapter 8 led to improved prediction of interface thermal conductance from first principles calculations. Toward the second point, for a model system of packed particles, significant headway was made in implementing numerical algorithms and collecting data to justify the approach in terms of highlighting the phenomena at play and pointing the way forward in developing and informing the kind of modeling approach originally envisioned (see Chapter 6). In

  14. Final Progress Report: FRACTURE AND SUBCRITICAL DEBONDING IN THIN LAYERED STRUCTURES: EXPERIMENTS AND MULTI-SCALE MODELING

    SciTech Connect

    Reinhold H. Dauskardt

    2005-08-30

    Final technical report detailing unique experimental and multi-scale computational modeling capabilities developed to study fracture and subcritical cracking in thin-film structures. Our program to date at Stanford has studied the mechanisms of fracture and fatigue crack-growth in structural ceramics at high temperature, bulk and thin-film glasses in selected moist environments where we demonstrated the presence of a true mechanical fatigue effect in some glass compositions. We also reported on the effects of complex environments and fatigue loading on subcritical cracking that effects the reliability of MEMS and other micro-devices using novel micro-machined silicon specimens and nanomaterial layers.

  15. A multi-scale model of the oxygen reduction reaction on highly active graphene nanosheets in alkaline conditions

    NASA Astrophysics Data System (ADS)

    Vazquez-Arenas, Jorge; Ramos-Sanchez, Guadalupe; Franco, Alejandro A.

    2016-10-01

    A multi-scale model based on a mean field approach, is proposed to describe the ORR mechanism on N-GN catalysts in alkaline media. The model implements activation energies calculated with Density Functional Theory (DFT) at the atomistic level, and scales up them into a continuum framework describing the cathode/electrolyte interface at the mesoscale level. The model also considers mass and momentum transports arising in the region next to the rotating electrode for all ionic species and O2; correction of potential drop and electrochemical double-layer capacitance. Most fitted parameters describing the kinetics of ORR elementary reactions are sensitive in the multi-scale model, which results from the incorporation of activation energies using the mean field method, unlike single-scale modelling Errors in the deviations from activation energies are found to be moderate, except for the elementary step (2) related to the formation of O2ads, which can be assigned to the inherent DFT limitations. The consumption of O2ads to form OOHads is determined as the rate-determining step as a result of its highest energy barrier (163.10 kJ mol-1) in the system, the largest error obtained for the deviation from activation energy (28.15%), and high sensitivity. This finding is confirmed with the calculated surface concentration and coverage of electroactive species.

  16. Magnetic hysteresis at the domain scale of a multi-scale material model for magneto-elastic behaviour

    NASA Astrophysics Data System (ADS)

    Vanoost, D.; Steentjes, S.; Peuteman, J.; Gielen, G.; De Gersem, H.; Pissoort, D.; Hameyer, K.

    2016-09-01

    This paper proposes a multi-scale energy-based material model for poly-crystalline materials. Describing the behaviour of poly-crystalline materials at three spatial scales of dominating physical mechanisms allows accounting for the heterogeneity and multi-axiality of the material behaviour. The three spatial scales are the poly-crystalline, grain and domain scale. Together with appropriate scale transitions rules and models for local magnetic behaviour at each scale, the model is able to describe the magneto-elastic behaviour (magnetostriction and hysteresis) at the macroscale, although the data input is merely based on a set of physical constants. Introducing a new energy density function that describes the demagnetisation field, the anhysteretic multi-scale energy-based material model is extended to the hysteretic case. The hysteresis behaviour is included at the domain scale according to the micro-magnetic domain theory while preserving a valid description for the magneto-elastic coupling. The model is verified using existing measurement data for different mechanical stress levels.

  17. Multi-scale modeling of Arabidopsis thaliana response to different CO2 conditions: From gene expression to metabolic flux.

    PubMed

    Liu, Lin; Shen, Fangzhou; Xin, Changpeng; Wang, Zhuo

    2016-01-01

    Multi-scale investigation from gene transcript level to metabolic activity is important to uncover plant response to environment perturbation. Here we integrated a genome-scale constraint-based metabolic model with transcriptome data to explore Arabidopsis thaliana response to both elevated and low CO2 conditions. The four condition-specific models from low to high CO2 concentrations show differences in active reaction sets, enriched pathways for increased/decreased fluxes, and putative post-transcriptional regulation, which indicates that condition-specific models are necessary to reflect physiological metabolic states. The simulated CO2 fixation flux at different CO2 concentrations is consistent with the measured Assimilation-CO2intercellular curve. Interestingly, we found that reactions in primary metabolism are affected most significantly by CO2 perturbation, whereas secondary metabolic reactions are not influenced a lot. The changes predicted in key pathways are consistent with existing knowledge. Another interesting point is that Arabidopsis is required to make stronger adjustment on metabolism to adapt to the more severe low CO2 stress than elevated CO2 . The challenges of identifying post-transcriptional regulation could also be addressed by the integrative model. In conclusion, this innovative application of multi-scale modeling in plants demonstrates potential to uncover the mechanisms of metabolic response to different conditions.

  18. Modeling Complex Biological Flows in Multi-Scale Systems using the APDEC Framework

    SciTech Connect

    Trebotich, D

    2006-06-24

    We have developed advanced numerical algorithms to model biological fluids in multiscale flow environments using the software framework developed under the SciDAC APDEC ISIC. The foundation of our computational effort is an approach for modeling DNA-laden fluids as ''bead-rod'' polymers whose dynamics are fully coupled to an incompressible viscous solvent. The method is capable of modeling short range forces and interactions between particles using soft potentials and rigid constraints. Our methods are based on higher-order finite difference methods in complex geometry with adaptivity, leveraging algorithms and solvers in the APDEC Framework. Our Cartesian grid embedded boundary approach to incompressible viscous flow in irregular geometries has also been interfaced to a fast and accurate level-sets method within the APDEC Framework for extracting surfaces from volume renderings of medical image data and used to simulate cardio-vascular and pulmonary flows in critical anatomies.

  19. A method of aggregating heterogeneous subgrid land cover input data for multi-scale urban parameterization within atmospheric models

    NASA Astrophysics Data System (ADS)

    Shaffer, S. R.

    2015-12-01

    A method for representing grid-scale heterogeneous development density for urban climate models from probability density functions of sub-grid resolution observed data is proposed. Derived values are evaluated in relation to normalized Shannon Entropy to provide guidance in assessing model input data. Urban fraction for dominant and mosaic urban class contributions are estimated by combining analysis of 30-meter resolution National Land Cover Database 2006 data products for continuous impervious surface area and categorical land cover. The method aims at reducing model error through improvement of urban parameterization and representation of observations employed as input data. The multi-scale variation of parameter values are demonstrated for several methods of utilizing input. The method provides multi-scale and spatial guidance for determining where parameterization schemes may be mis-representing heterogeneity of input data, along with motivation for employing mosaic techniques based upon assessment of input data. The proposed method has wider potential for geographic application, and complements data products which focus on characterizing central business districts. The method enables obtaining urban fraction dependent upon resolution and class partition scheme, based upon improved parameterization of observed data, which provides one means of influencing simulation prediction at various aggregated grid scales.

  20. Development of the multi-scale model for urban climate analysis and evaluation of urban greening effects on energy consumption

    NASA Astrophysics Data System (ADS)

    Hamano, H.; Nakayama, T.; Fujita, T.; Hori, H.; Tagami, H.

    2009-12-01

    It is necessary to reduce Greenhouse gases (GHG) emissions drastically to stabilize climate change, and Japan is also required to assess its long-term global warming policy. In achieving the low carbon society and sustainable cities, the numerical evaluation of environmental impacts of the application of different technologies and policies was preliminarily examined by utilizing integrative urban environmental model. This research aims to develop the multi-scale model for urban climate analysis and to evaluate the urban greening effects on energy consumption from household and business sectors. It developed the multi-scale model combined the process-based NIES integrated catchment-based eco-hydrology (NICE) model with the meso-scale meteorological model (Regional Atmospheric Modeling System : RAMS) and urban canopy model to estimate the urban climate mitigation effects by introduction of urban heat environmental mitigation technology and scenario. The numerical simulation conducted with the multi-scale level horizontally consisting regional scale (260×260km with 2km grid) and urban area scale (36×26km with 0.2km grid) against the objective area, Kawasaki city of Japan. The urban canopy model predicts the three dimensional atmospheric conditions including anthropogenic heat effect from household, business and factory sectors. Furthermore the tile method applied into the urban canopy model for the improvement of numerical accuracy and detailed land use information in each grid. The validation of this model was conducted by comparison with the observed air temperature of 29 points in entire Kawasaki area from 1st to 31th of August, 2006. From the quantitative validation of model performance, the coefficient of correlation was 0.72 and the root mean square error was 2.99C. The introduction of patch method into urban canopy model made it possible to calculate the each land use effect, and the accuracy of predicted results was improved against the land use area

  1. Simulated village locations in Thailand: A multi-scale model including a neural network approach

    PubMed Central

    Malanson, George P.; Entwisle, Barbara

    2010-01-01

    The simulation of rural land use systems, in general, and rural settlement dynamics in particular has developed with synergies of theory and methods for decades. Three current issues are: linking spatial patterns and processes, representing hierarchical relations across scales, and considering nonlinearity to address complex non-stationary settlement dynamics. We present a hierarchical simulation model to investigate complex rural settlement dynamics in Nang Rong, Thailand. This simulation uses sub-models to allocate new villages at three spatial scales. Regional and sub-regional models, which involve a nonlinear space-time autoregressive model implemented in a neural network approach, determine the number of new villages to be established. A dynamic village niche model, establishing pattern-process link, was designed to enable the allocation of villages into specific locations. Spatiotemporal variability in model performance indicates the pattern of village location changes as a settlement frontier advances from rice-growing lowlands to higher elevations. Experiments results demonstrate this simulation model can enhance our understanding of settlement development in Nang Rong and thus gain insight into complex land use systems in this area. PMID:21399748

  2. Concurrent multi-scale design optimization of composite frame structures using the Heaviside penalization of discrete material model

    NASA Astrophysics Data System (ADS)

    Yan, Jun; Duan, Zunyi; Lund, Erik; Zhao, Guozhong

    2016-06-01

    This paper deals with the concurrent multi-scale optimization design of frame structure composed of glass or carbon fiber reinforced polymer laminates. In the composite frame structure, the fiber winding angle at the micro-material scale and the geometrical parameter of components of the frame in the macro-structural scale are introduced as the independent variables on the two geometrical scales. Considering manufacturing requirements, discrete fiber winding angles are specified for the micro design variable. The improved Heaviside penalization discrete material optimization interpolation scheme has been applied to achieve the discrete optimization design of the fiber winding angle. An optimization model based on the minimum structural compliance and the specified fiber material volume constraint has been established. The sensitivity information about the two geometrical scales design variables are also deduced considering the characteristics of discrete fiber winding angles. The optimization results of the fiber winding angle or the macro structural topology on the two single geometrical scales, together with the concurrent two-scale optimization, is separately studied and compared in the paper. Numerical examples in the paper show that the concurrent multi-scale optimization can further explore the coupling effect between the macro-structure and micro-material of the composite to achieve an ultra-light design of the composite frame structure. The novel two geometrical scales optimization model provides a new opportunity for the design of composite structure in aerospace and other industries.

  3. Uncertainty Quantification and Management for Multi-scale Nuclear Materials Modeling

    SciTech Connect

    McDowell, David; Deo, Chaitanya; Zhu, Ting; Wang, Yan

    2015-10-21

    Understanding and improving microstructural mechanical stability in metals and alloys is central to the development of high strength and high ductility materials for cladding and cores structures in advanced fast reactors. Design and enhancement of radiation-induced damage tolerant alloys are facilitated by better understanding the connection of various unit processes to collective responses in a multiscale model chain, including: dislocation nucleation, absorption and desorption at interfaces; vacancy production, radiation-induced segregation of Cr and Ni at defect clusters (point defect sinks) in BCC Fe-Cr ferritic/martensitic steels; investigation of interaction of interstitials and vacancies with impurities (V, Nb, Ta, Mo, W, Al, Si, P, S); time evolution of swelling (cluster growth) phenomena of irradiated materials; and energetics and kinetics of dislocation bypass of defects formed by interstitial clustering and formation of prismatic loops, informing statistical models of continuum character with regard to processes of dislocation glide, vacancy agglomeration and swelling, climb and cross slip.

  4. Multi-scale modelling of supercapacitors: From molecular simulations to a transmission line model

    NASA Astrophysics Data System (ADS)

    Pean, C.; Rotenberg, B.; Simon, P.; Salanne, M.

    2016-09-01

    We perform molecular dynamics simulations of a typical nanoporous-carbon based supercapacitor. The organic electrolyte consists in 1-ethyl-3-methylimidazolium and hexafluorophosphate ions dissolved in acetonitrile. We simulate systems at equilibrium, for various applied voltages. This allows us to determine the relevant thermodynamic (capacitance) and transport (in-pore resistivities) properties. These quantities are then injected in a transmission line model for testing its ability to predict the charging properties of the device. The results from this macroscopic model are in good agreement with non-equilibrium molecular dynamics simulations, which validates its use for interpreting electrochemical impedance experiments.

  5. Stress-resultant models for ultimate load design of reinforced concrete frames and multi-scale parameter estimates

    NASA Astrophysics Data System (ADS)

    Pham, B. H.; Brancherie, D.; Davenne, L.; Ibrahimbegovic, A.

    2013-03-01

    In this work, we present a new finite element for (geometrically linear) Timoshenko beam model for ultimate load computation of reinforced concrete frames. The proposed model combines the descriptions of the diffuse plastic failure in the beam-column followed by the creation of plastic hinges due to the failure or collapse of the concrete and of the re-bars. A modified multi-scale analysis is performed in order to identify the parameters for stress-resultant-based macro model, which is used to described the behavior of the Timoshenko beam element. For clarity, we focus upon the micro-scale models using the multi-fiber elements with embedded displacement discontinuities in mode I, which would typically be triggered by bending failure mode. More general case of micro-scale model capable of describing shear failure is described by Ibrahimbegovic et al. (Int J Numer Methods Eng 83(4):452-481, 2010).

  6. Multi-Scale Modeling, Surrogate-Based Analysis, and Optimization of Lithium-Ion Batteries for Vehicle Applications

    NASA Astrophysics Data System (ADS)

    Du, Wenbo

    A common attribute of electric-powered aerospace vehicles and systems such as unmanned aerial vehicles, hybrid- and fully-electric aircraft, and satellites is that their performance is usually limited by the energy density of their batteries. Although lithium-ion batteries offer distinct advantages such as high voltage and low weight over other battery technologies, they are a relatively new development, and thus significant gaps in the understanding of the physical phenomena that govern battery performance remain. As a result of this limited understanding, batteries must often undergo a cumbersome design process involving many manual iterations based on rules of thumb and ad-hoc design principles. A systematic study of the relationship between operational, geometric, morphological, and material-dependent properties and performance metrics such as energy and power density is non-trivial due to the multiphysics, multiphase, and multiscale nature of the battery system. To address these challenges, two numerical frameworks are established in this dissertation: a process for analyzing and optimizing several key design variables using surrogate modeling tools and gradient-based optimizers, and a multi-scale model that incorporates more detailed microstructural information into the computationally efficient but limited macro-homogeneous model. In the surrogate modeling process, multi-dimensional maps for the cell energy density with respect to design variables such as the particle size, ion diffusivity, and electron conductivity of the porous cathode material are created. A combined surrogate- and gradient-based approach is employed to identify optimal values for cathode thickness and porosity under various operating conditions, and quantify the uncertainty in the surrogate model. The performance of multiple cathode materials is also compared by defining dimensionless transport parameters. The multi-scale model makes use of detailed 3-D FEM simulations conducted at the

  7. The North American Carbon Program Multi-scale Synthesis and Terrestrial Model Intercomparison Project – Part 2: Environmental driver data

    DOE PAGES

    Wei, Yaxing; Liu, Shishi; Huntzinger, Deborah N.; Michalak, Anna M.; Viovy, Nicolas; Post, Wilfred M.; Schwalm, Christopher R.; Schaeffer, Kevin; Jacobson, Andrew R.; Lu, Chaoqun; et al

    2014-12-05

    Ecosystems are important and dynamic components of the global carbon cycle, and terrestrial biospheric models (TBMs) are crucial tools in further understanding of how terrestrial carbon is stored and exchanged with the atmosphere across a variety of spatial and temporal scales. Improving TBM skills, and quantifying and reducing their estimation uncertainties, pose significant challenges. The Multi-scale Synthesis and Terrestrial Model Intercomparison Project (MsTMIP) is a formal multi-scale and multi-model intercomparison effort set up to tackle these challenges. The MsTMIP protocol prescribes standardized environmental driver data that are shared among model teams to facilitate model model and model observation comparisons. Inmore » this article, we describe the global and North American environmental driver data sets prepared for the MsTMIP activity to both support their use in MsTMIP and make these data, along with the processes used in selecting/processing these data, accessible to a broader audience. Based on project needs and lessons learned from past model intercomparison activities, we compiled climate, atmospheric CO2 concentrations, nitrogen deposition, land use and land cover change (LULCC), C3 / C4 grasses fractions, major crops, phenology and soil data into a standard format for global (0.5⁰ x 0.5⁰ resolution) and regional (North American: 0.25⁰ x 0.25⁰ resolution) simulations. In order to meet the needs of MsTMIP, improvements were made to several of the original environmental data sets, by improving the quality, and/or changing their spatial and temporal coverage, and resolution. The resulting standardized model driver data sets are being used by over 20 different models participating in MsTMIP. Lastly, the data are archived at the Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC, http://daac.ornl.gov) to provide long-term data management and distribution.« less

  8. The North American Carbon Program Multi-scale Synthesis and Terrestrial Model Intercomparison Project – Part 2: Environmental driver data

    SciTech Connect

    Wei, Yaxing; Liu, Shishi; Huntzinger, Deborah N.; Michalak, Anna M.; Viovy, Nicolas; Post, Wilfred M.; Schwalm, Christopher R.; Schaeffer, Kevin; Jacobson, Andrew R.; Lu, Chaoqun; Tian, Hanqin; Ricciuto, Daniel M.; Cook, Robert B.; Mao, Jiafu; Shi, Xiaoying

    2014-12-05

    Ecosystems are important and dynamic components of the global carbon cycle, and terrestrial biospheric models (TBMs) are crucial tools in further understanding of how terrestrial carbon is stored and exchanged with the atmosphere across a variety of spatial and temporal scales. Improving TBM skills, and quantifying and reducing their estimation uncertainties, pose significant challenges. The Multi-scale Synthesis and Terrestrial Model Intercomparison Project (MsTMIP) is a formal multi-scale and multi-model intercomparison effort set up to tackle these challenges. The MsTMIP protocol prescribes standardized environmental driver data that are shared among model teams to facilitate model model and model observation comparisons. In this article, we describe the global and North American environmental driver data sets prepared for the MsTMIP activity to both support their use in MsTMIP and make these data, along with the processes used in selecting/processing these data, accessible to a broader audience. Based on project needs and lessons learned from past model intercomparison activities, we compiled climate, atmospheric CO2 concentrations, nitrogen deposition, land use and land cover change (LULCC), C3 / C4 grasses fractions, major crops, phenology and soil data into a standard format for global (0.5⁰ x 0.5⁰ resolution) and regional (North American: 0.25⁰ x 0.25⁰ resolution) simulations. In order to meet the needs of MsTMIP, improvements were made to several of the original environmental data sets, by improving the quality, and/or changing their spatial and temporal coverage, and resolution. The resulting standardized model driver data sets are being used by over 20 different models participating in MsTMIP. Lastly, the data are archived at the Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC, http://daac.ornl.gov) to provide long-term data management and distribution.

  9. The North American Carbon Program Multi-scale Synthesis and Terrestrial Model Intercomparison Project - Part 2: Environmental driver data

    NASA Astrophysics Data System (ADS)

    Wei, Y.; Liu, S.; Huntzinger, D. N.; Michalak, A. M.; Viovy, N.; Post, W. M.; Schwalm, C. R.; Schaefer, K.; Jacobson, A. R.; Lu, C.; Tian, H.; Ricciuto, D. M.; Cook, R. B.; Mao, J.; Shi, X.

    2013-11-01

    Ecosystems are important and dynamic components of the global carbon cycle, and terrestrial biospheric models (TBMs) are crucial tools in further understanding of how terrestrial carbon is stored and exchanged with the atmosphere across a variety of spatial and temporal scales. Improving TBM model skills, and quantifying and reducing their estimation uncertainties, pose significant challenges. The Multi-scale Synthesis and Terrestrial Model Intercomparison Project (MsTMIP) is a formal multi-scale and multi-model intercomparison effort set up to tackle these challenges. The MsTMIP protocol prescribes standardized environmental driver data that are shared among model teams to facilitate model-model and model-observation comparisons. This paper describes the global and North American environmental driver data sets prepared for the MsTMIP activity to both support their use in MsTMIP and make these data, along with the processes used in selecting/processing these data, accessible to a broader audience. Based on project needs, we compiled climate, atmospheric CO2 concentrations, nitrogen deposition, land-use and land-cover change (LULCC), C3/C4 grasses fractions, major crops, phenology, and soil data into a standard format for global (0.5° x 0.5° resolution) and regional (North American, 0.25° x 0.25° resolution) simulations. In order to meet the needs of MsTMIP, improvements were made to several of the original environmental data sets, by changing the quality, the spatial and temporal coverage, resolution, or a combination of these. The resulting standardized model driver data sets are being used by over 20 different models participating MsTMIP. The data are archived at the Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC, http://daac.ornl.gov) to provide long-term data management and distribution.

  10. The North American Carbon Program Multi-scale Synthesis and Terrestrial Model Intercomparison Project - Part 2: Environmental driver data

    NASA Astrophysics Data System (ADS)

    Wei, Y.; Liu, S.; Huntzinger, D. N.; Michalak, A. M.; Viovy, N.; Post, W. M.; Schwalm, C. R.; Schaefer, K.; Jacobson, A. R.; Lu, C.; Tian, H.; Ricciuto, D. M.; Cook, R. B.; Mao, J.; Shi, X.

    2014-12-01

    Ecosystems are important and dynamic components of the global carbon cycle, and terrestrial biospheric models (TBMs) are crucial tools in further understanding of how terrestrial carbon is stored and exchanged with the atmosphere across a variety of spatial and temporal scales. Improving TBM skills, and quantifying and reducing their estimation uncertainties, pose significant challenges. The Multi-scale Synthesis and Terrestrial Model Intercomparison Project (MsTMIP) is a formal multi-scale and multi-model intercomparison effort set up to tackle these challenges. The MsTMIP protocol prescribes standardized environmental driver data that are shared among model teams to facilitate model-model and model-observation comparisons. This paper describes the global and North American environmental driver data sets prepared for the MsTMIP activity to both support their use in MsTMIP and make these data, along with the processes used in selecting/processing these data, accessible to a broader audience. Based on project needs and lessons learned from past model intercomparison activities, we compiled climate, atmospheric CO2 concentrations, nitrogen deposition, land use and land cover change (LULCC), C3 / C4 grasses fractions, major crops, phenology and soil data into a standard format for global (0.5° × 0.5° resolution) and regional (North American: 0.25° × 0.25° resolution) simulations. In order to meet the needs of MsTMIP, improvements were made to several of the original environmental data sets, by improving the quality, and/or changing their spatial and temporal coverage, and resolution. The resulting standardized model driver data sets are being used by over 20 different models participating in MsTMIP. The data are archived at the Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC, http://daac.ornl.gov) to provide long-term data management and distribution.

  11. Multi-Scale Hydrometeorological Modeling, Land Data Assimilation and Parameter Estimation with the Land Information System

    NASA Technical Reports Server (NTRS)

    Peters-Lidard, Christa D.

    2011-01-01

    The Land Information System (LIS; http://lis.gsfc.nasa.gov) is a flexible land surface modeling framework that has been developed with the goal of integrating satellite-and ground-based observational data products and advanced land surface modeling techniques to produce optimal fields of land surface states and fluxes. As such, LIS represents a step towards the next generation land component of an integrated Earth system model. In recognition of LIS object-oriented software design, use and impact in the land surface and hydrometeorological modeling community, the LIS software was selected as a co-winner of NASA?s 2005 Software of the Year award.LIS facilitates the integration of observations from Earth-observing systems and predictions and forecasts from Earth System and Earth science models into the decision-making processes of partnering agency and national organizations. Due to its flexible software design, LIS can serve both as a Problem Solving Environment (PSE) for hydrologic research to enable accurate global water and energy cycle predictions, and as a Decision Support System (DSS) to generate useful information for application areas including disaster management, water resources management, agricultural management, numerical weather prediction, air quality and military mobility assessment. LIS has e volved from two earlier efforts -- North American Land Data Assimilation System (NLDAS) and Global Land Data Assimilation System (GLDAS) that focused primarily on improving numerical weather prediction skills by improving the characterization of the land surface conditions. Both of GLDAS and NLDAS now use specific configurations of the LIS software in their current implementations.In addition, LIS was recently transitioned into operations at the US Air Force Weather Agency (AFWA) to ultimately replace their Agricultural Meteorology (AGRMET) system, and is also used routinely by NOAA's National Centers for Environmental Prediction (NCEP)/Environmental Modeling

  12. Multi-Scale Hydrometeorological Modeling, Land Data Assimilation and Parameter Estimation with the Land Information System

    NASA Technical Reports Server (NTRS)

    Peters-Lidard, Christa D.; Kumar, Sujay V.; Santanello, Joseph A., Jr.; Reichle, Rolf H.

    2009-01-01

    The Land Information System (LIS; http://lis.gsfc.nasa.gov; Kumar et al., 2006; Peters- Lidard et al.,2007) is a flexible land surface modeling framework that has been developed with the goal of integrating satellite- and ground-based observational data products and advanced land surface modeling techniques to produce optimal fields of land surface states and fluxes. As such, LIS represents a step towards the next generation land component of an integrated Earth system model. In recognition of LIS object-oriented software design, use and impact in the land surface and hydrometeorological modeling community, the LIS software was selected ase co-winner of NASA's 2005 Software of the Year award. LIS facilitates the integration of observations from Earth-observing systems and predictions and forecasts from Earth System and Earth science models into the decision-making processes of partnering agency and national organizations. Due to its flexible software design, LIS can serve both as a Problem Solving Environment (PSE) for hydrologic research to enable accurate global water and energy cycle predictions, and as a Decision Support System (DSS) to generate useful information for application areas including disaster management, water resources management, agricultural management, numerical weather prediction, air quality and military mobility assessment. LIS has evolved from two earlier efforts North American Land Data Assimilation System (NLDAS; Mitchell et al. 2004) and Global Land Data Assimilation System (GLDAS; Rodell al. 2004) that focused primarily on improving numerical weather prediction skills by improving the characterization of the land surface conditions. Both of GLDAS and NLDAS now use specific configurations of the LIS software in their current implementations. In addition, LIS was recently transitioned into operations at the US Air Force Weather Agency (AFWA) to ultimately replace their Agricultural Meteorology (AGRMET) system, and is also used routinely by

  13. Posterior predictive modeling using multi-scale stochastic inverse parameter estimates.

    SciTech Connect

    Waanders, Bart Van Bloemen; Marzouk, Youssef M.; Ray, Jaideep; McKenna, Sean Andrew

    2010-12-01

    Multi-scale binary permeability field estimation from static and dynamic data is completed using Markov Chain Monte Carlo (MCMC) sampling. The binary permeability field is defined as high permeability inclusions within a lower permeability matrix. Static data are obtained as measurements of permeability with support consistent to the coarse scale discretization. Dynamic data are advective travel times along streamlines calculated through a fine-scale field and averaged for each observation point at the coarse scale. Parameters estimated at the coarse scale (30 x 20 grid) are the spatially varying proportion of the high permeability phase and the inclusion length and aspect ratio of the high permeability inclusions. From the non-parametric, posterior distributions estimated for these parameters, a recently developed sub-grid algorithm is employed to create an ensemble of realizations representing the fine-scale (3000 x 2000), binary permeability field. Each fine-scale ensemble member is instantiated by convolution of an uncorrelated multiGaussian random field with a Gaussian kernel defined by the estimated inclusion length and aspect ratio. Since the multiGaussian random field is itself a realization of a stochastic process, the procedure for generating fine-scale binary permeability field realizations is also stochastic. Two different methods are hypothesized to perform posterior predictive tests. Different mechanisms for combining multi Gaussian random fields with kernels defined from the MCMC sampling are examined. Posterior predictive accuracy of the estimated parameters is assessed against a simulated ground truth for predictions at both the coarse scale (effective permeabilities) and at the fine scale (advective travel time distributions). The two techniques for conducting posterior predictive tests are compared by their ability to recover the static and dynamic data. The skill of the inference and the method for generating fine-scale binary permeability

  14. MULTI-SCALE MODELING AND APPROXIMATION ASSISTED OPTIMIZATION OF BARE TUBE HEAT EXCHANGERS

    SciTech Connect

    Bacellar, Daniel; Ling, Jiazhen; Aute, Vikrant; Radermacher, Reinhard; Abdelaziz, Omar

    2014-01-01

    Air-to-refrigerant heat exchangers are very common in air-conditioning, heat pump and refrigeration applications. In these heat exchangers, there is a great benefit in terms of size, weight, refrigerant charge and heat transfer coefficient, by moving from conventional channel sizes (~ 9mm) to smaller channel sizes (< 5mm). This work investigates new designs for air-to-refrigerant heat exchangers with tube outer diameter ranging from 0.5 to 2.0mm. The goal of this research is to develop and optimize the design of these heat exchangers and compare their performance with existing state of the art designs. The air-side performance of various tube bundle configurations are analyzed using a Parallel Parameterized CFD (PPCFD) technique. PPCFD allows for fast-parametric CFD analyses of various geometries with topology change. Approximation techniques drastically reduce the number of CFD evaluations required during optimization. Maximum Entropy Design method is used for sampling and Kriging method is used for metamodeling. Metamodels are developed for the air-side heat transfer coefficients and pressure drop as a function of tube-bundle dimensions and air velocity. The metamodels are then integrated with an air-to-refrigerant heat exchanger design code. This integration allows a multi-scale analysis of air-side performance heat exchangers including air-to-refrigerant heat transfer and phase change. Overall optimization is carried out using a multi-objective genetic algorithm. The optimal designs found can exhibit 50 percent size reduction, 75 percent decrease in air side pressure drop and doubled air heat transfer coefficients compared to a high performance compact micro channel heat exchanger with same capacity and flow rates.

  15. Basilar membrane and reticular lamina motion in a multi-scale finite element model of the mouse cochlea

    NASA Astrophysics Data System (ADS)

    Soons, Joris; Dirckx, Joris; Steele, Charles; Puria, Sunil

    2015-12-01

    A multi-scale finite element (FE) model of the mouse cochlea, based on its anatomy and material properties is presented. The important feature in the model is a lattice of 400 Y-shaped structures in the longitudinal direction, each formed by Deiters cells, phalangeal processes and outer hair cells (OHC). OHC somatic motility is modeled by an expansion force proportional to the shear on the stereocilia, which in turn is proportional to the pressure difference between the scala vestibule and scala tympani. Basilar membrane (BM) and reticular lamina (RL) velocity compare qualitatively very well with recent in vivo measurements in guinea pig [2]. Compared to the BM, the RL is shown to have higher amplification and a shift to higher frequencies. This comes naturally from the realistic Y-shaped cell organization without tectorial membrane tuning.

  16. Predicting Species Distributions Using Record Centre Data: Multi-Scale Modelling of Habitat Suitability for Bat Roosts

    PubMed Central

    Bellamy, Chloe; Altringham, John

    2015-01-01

    Conservation increasingly operates at the landscape scale. For this to be effective, we need landscape scale information on species distributions and the environmental factors that underpin them. Species records are becoming increasingly available via data centres and online portals, but they are often patchy and biased. We demonstrate how such data can yield useful habitat suitability models, using bat roost records as an example. We analysed the effects of environmental variables at eight spatial scales (500 m – 6 km) on roost selection by eight bat species (Pipistrellus pipistrellus, P. pygmaeus, Nyctalus noctula, Myotis mystacinus, M. brandtii, M. nattereri, M. daubentonii, and Plecotus auritus) using the presence-only modelling software MaxEnt. Modelling was carried out on a selection of 418 data centre roost records from the Lake District National Park, UK. Target group pseudoabsences were selected to reduce the impact of sampling bias. Multi-scale models, combining variables measured at their best performing spatial scales, were used to predict roosting habitat suitability, yielding models with useful predictive abilities. Small areas of deciduous woodland consistently increased roosting habitat suitability, but other habitat associations varied between species and scales. Pipistrellus were positively related to built environments at small scales, and depended on large-scale woodland availability. The other, more specialist, species were highly sensitive to human-altered landscapes, avoiding even small rural towns. The strength of many relationships at large scales suggests that bats are sensitive to habitat modifications far from the roost itself. The fine resolution, large extent maps will aid targeted decision-making by conservationists and planners. We have made available an ArcGIS toolbox that automates the production of multi-scale variables, to facilitate the application of our methods to other taxa and locations. Habitat suitability modelling has

  17. Predicting Species Distributions Using Record Centre Data: Multi-Scale Modelling of Habitat Suitability for Bat Roosts.

    PubMed

    Bellamy, Chloe; Altringham, John

    2015-01-01

    Conservation increasingly operates at the landscape scale. For this to be effective, we need landscape scale information on species distributions and the environmental factors that underpin them. Species records are becoming increasingly available via data centres and online portals, but they are often patchy and biased. We demonstrate how such data can yield useful habitat suitability models, using bat roost records as an example. We analysed the effects of environmental variables at eight spatial scales (500 m - 6 km) on roost selection by eight bat species (Pipistrellus pipistrellus, P. pygmaeus, Nyctalus noctula, Myotis mystacinus, M. brandtii, M. nattereri, M. daubentonii, and Plecotus auritus) using the presence-only modelling software MaxEnt. Modelling was carried out on a selection of 418 data centre roost records from the Lake District National Park, UK. Target group pseudoabsences were selected to reduce the impact of sampling bias. Multi-scale models, combining variables measured at their best performing spatial scales, were used to predict roosting habitat suitability, yielding models with useful predictive abilities. Small areas of deciduous woodland consistently increased roosting habitat suitability, but other habitat associations varied between species and scales. Pipistrellus were positively related to built environments at small scales, and depended on large-scale woodland availability. The other, more specialist, species were highly sensitive to human-altered landscapes, avoiding even small rural towns. The strength of many relationships at large scales suggests that bats are sensitive to habitat modifications far from the roost itself. The fine resolution, large extent maps will aid targeted decision-making by conservationists and planners. We have made available an ArcGIS toolbox that automates the production of multi-scale variables, to facilitate the application of our methods to other taxa and locations. Habitat suitability modelling has the

  18. Multi-scale diffuse interface modeling of multi-component two-phase flow with partial miscibility

    NASA Astrophysics Data System (ADS)

    Kou, Jisheng; Sun, Shuyu

    2016-08-01

    In this paper, we introduce a diffuse interface model to simulate multi-component two-phase flow with partial miscibility based on a realistic equation of state (e.g. Peng-Robinson equation of state). Because of partial miscibility, thermodynamic relations are used to model not only interfacial properties but also bulk properties, including density, composition, pressure, and realistic viscosity. As far as we know, this effort is the first time to use diffuse interface modeling based on equation of state for modeling of multi-component two-phase flow with partial miscibility. In numerical simulation, the key issue is to resolve the high contrast of scales from the microscopic interface composition to macroscale bulk fluid motion since the interface has a nanoscale thickness only. To efficiently solve this challenging problem, we develop a multi-scale simulation method. At the microscopic scale, we deduce a reduced interfacial equation under reasonable assumptions, and then we propose a formulation of capillary pressure, which is consistent with macroscale flow equations. Moreover, we show that Young-Laplace equation is an approximation of this capillarity formulation, and this formulation is also consistent with the concept of Tolman length, which is a correction of Young-Laplace equation. At the macroscopical scale, the interfaces are treated as discontinuous surfaces separating two phases of fluids. Our approach differs from conventional sharp-interface two-phase flow model in that we use the capillary pressure directly instead of a combination of surface tension and Young-Laplace equation because capillarity can be calculated from our proposed capillarity formulation. A compatible condition is also derived for the pressure in flow equations. Furthermore, based on the proposed capillarity formulation, we design an efficient numerical method for directly computing the capillary pressure between two fluids composed of multiple components. Finally, numerical tests

  19. Multi-scale modeling of microstructure dependent intergranular brittle fracture using a quantitative phase-field based method

    DOE PAGES

    Chakraborty, Pritam; Zhang, Yongfeng; Tonks, Michael R.

    2015-12-07

    In this study, the fracture behavior of brittle materials is strongly influenced by their underlying microstructure that needs explicit consideration for accurate prediction of fracture properties and the associated scatter. In this work, a hierarchical multi-scale approach is pursued to model microstructure sensitive brittle fracture. A quantitative phase-field based fracture model is utilized to capture the complex crack growth behavior in the microstructure and the related parameters are calibrated from lower length scale atomistic simulations instead of engineering scale experimental data. The workability of this approach is demonstrated by performing porosity dependent intergranular fracture simulations in UO2 and comparing themore » predictions with experiments.« less

  20. A Unified Multi-scale Model for Cross-Scale Evaluation and Integration of Hydrological and Biogeochemical Processes

    NASA Astrophysics Data System (ADS)

    Liu, C.; Yang, X.; Bailey, V. L.; Bond-Lamberty, B. P.; Hinkle, C.

    2013-12-01

    Mathematical representations of hydrological and biogeochemical processes in soil, plant, aquatic, and atmospheric systems vary with scale. Process-rich models are typically used to describe hydrological and biogeochemical processes at the pore and small scales, while empirical, correlation approaches are often used at the watershed and regional scales. A major challenge for multi-scale modeling is that water flow, biogeochemical processes, and reactive transport are described using different physical laws and/or expressions at the different scales. For example, the flow is governed by the Navier-Stokes equations at the pore-scale in soils, by the Darcy law in soil columns and aquifer, and by the Navier-Stokes equations again in open water bodies (ponds, lake, river) and atmosphere surface layer. This research explores whether the physical laws at the different scales and in different physical domains can be unified to form a unified multi-scale model (UMSM) to systematically investigate the cross-scale, cross-domain behavior of fundamental processes at different scales. This presentation will discuss our research on the concept, mathematical equations, and numerical execution of the UMSM. Three-dimensional, multi-scale hydrological processes at the Disney Wilderness Preservation (DWP) site, Florida will be used as an example for demonstrating the application of the UMSM. In this research, the UMSM was used to simulate hydrological processes in rooting zones at the pore and small scales including water migration in soils under saturated and unsaturated conditions, root-induced hydrological redistribution, and role of rooting zone biogeochemical properties (e.g., root exudates and microbial mucilage) on water storage and wetting/draining. The small scale simulation results were used to estimate effective water retention properties in soil columns that were superimposed on the bulk soil water retention properties at the DWP site. The UMSM parameterized from smaller

  1. Multi-scale Modelling of bcc-Fe Based Alloys for Nuclear Applications

    SciTech Connect

    Malerba, Lorenzo

    2008-07-01

    , advanced techniques to fit interatomic potentials consistent with thermodynamics are proposed and the results of their application to the mentioned alloys are presented. Next, the development of advanced methods, based on the use of artificial intelligence, to improve both the physical reliability and the computational efficiency of kinetic Monte Carlo codes for the study of point-defect clustering and phase changes beyond the scale of MD, is reported. These recent progresses bear the promise of being able, in the near future, of producing reliable tools for the description of the microstructure evolution of realistic model alloys under irradiation. (author)

  2. Multi scale modeling of ignition and combustion of micro and nano aluminum particles

    NASA Astrophysics Data System (ADS)

    Puri, Puneesh

    With renewed interest in nano scale energetic materials like aluminum, many fundamental issues concerning the ignition and combustion characteristics at nano scales, remain to be clarified. The overall aim of the current study is the establishment of a unified theory accommodating the various processes and mechanisms involved in the combustion and ignition of aluminum particles at micro and nano scales. A comprehensive review on the ignition and combustion of aluminum particles at multi scales was first performed identifying various processes and mechanisms involved. Research focus was also placed on the establishment of a Molecular Dynamics (MD) simulation tool to investigate the characteristics of nano-particulate aluminum through three major studies. The general computational framework involved parallelized preprocessing, post-processing and main code with capability to simulate different ensembles using appropriate algorithms. Size dependence of melting temperature of pure aluminum particles was investigated in the first study. Phenomena like dynamic coexistence of solid and liquid phase and effect of surface charges on melting were explored. The second study involved the study of effect of defects in the form of voids on melting of bulk and particulate phase aluminum. The third MD study was used to analyze the thermo-mechanical behavior of nano-sized aluminum particles with total diameter of 5-10 nm and oxide thickness of 1-2.5 nm. The ensuing solid-solid and solid-liquid phase changes in the core and shell, stresses developed within the shell, and the diffusion of aluminum cations in the oxide layer, were explored in depth for amorphous and crystalline oxide layers. In the limiting case, the condition for pyrophoricity/explosivity of nano-particulate aluminum was analyzed and modified. The size dependence of thermodynamic properties at nano scales were considered and incorporated into the existing theories developed for micro and larger scales. Finally, a

  3. A multi-scale GIS and hydrodynamic modelling approach to fish passage assessment: Clarence and Shoalhaven Rivers, NSW Australia

    NASA Astrophysics Data System (ADS)

    Bonetti, Rita M.; Reinfelds, Ivars V.; Butler, Gavin L.; Walsh, Chris T.; Broderick, Tony J.; Chisholm, Laurie A.

    2016-05-01

    Natural barriers such as waterfalls, cascades, rapids and riffles limit the dispersal and in-stream range of migratory fish, yet little is known of the interplay between these gradient dependent landforms, their hydraulic characteristics and flow rates that facilitate fish passage. The resurgence of dam construction in numerous river basins world-wide provides impetus to the development of robust techniques for assessment of the effects of downstream flow regime changes on natural fish passage barriers and associated consequences as to the length of rivers available to migratory species. This paper outlines a multi-scale technique for quantifying the relative magnitude of natural fish passage barriers in river systems and flow rates that facilitate passage by fish. First, a GIS-based approach is used to quantify channel gradients for the length of river or reach under investigation from a high resolution DEM, setting the magnitude of identified passage barriers in a longer context (tens to hundreds of km). Second, LiDAR, topographic and bathymetric survey-based hydrodynamic modelling is used to assess flow rates that can be regarded as facilitating passage across specific barriers identified by the river to reach scale gradient analysis. Examples of multi-scale approaches to fish passage assessment for flood-flow and low-flow passage issues are provided from the Clarence and Shoalhaven Rivers, NSW, Australia. In these river systems, passive acoustic telemetry data on actual movements and migrations by Australian bass (Macquaria novemaculeata) provide a means of validating modelled assessments of flow rates associated with successful fish passage across natural barriers. Analysis of actual fish movements across passage barriers in these river systems indicates that two dimensional hydraulic modelling can usefully quantify flow rates associated with the facilitation of fish passage across natural barriers by a majority of individual fishes for use in management

  4. Directional Multi-scale Modeling of High-Resolution Computed Tomography (HRCT) Lung Images for Diffuse Lung Disease Classification

    NASA Astrophysics Data System (ADS)

    Vo, Kiet T.; Sowmya, Arcot

    A directional multi-scale modeling scheme based on wavelet and contourlet transforms is employed to describe HRCT lung image textures for classifying four diffuse lung disease patterns: normal, emphysema, ground glass opacity (GGO) and honey-combing. Generalized Gaussian density parameters are used to represent the detail sub-band features obtained by wavelet and contourlet transforms. In addition, support vector machines (SVMs) with excellent performance in a variety of pattern classification problems are used as classifier. The method is tested on a collection of 89 slices from 38 patients, each slice of size 512x512, 16 bits/pixel in DICOM format. The dataset contains 70,000 ROIs of those slices marked by experienced radiologists. We employ this technique at different wavelet and contourlet transform scales for diffuse lung disease classification. The technique presented here has best overall sensitivity 93.40% and specificity 98.40%.

  5. Modeling and simulation of multi-physics multi-scale transport phenomenain bio-medical applications

    NASA Astrophysics Data System (ADS)

    Kenjereš, Saša

    2014-08-01

    We present a short overview of some of our most recent work that combines the mathematical modeling, advanced computer simulations and state-of-the-art experimental techniques of physical transport phenomena in various bio-medical applications. In the first example, we tackle predictions of complex blood flow patterns in the patient-specific vascular system (carotid artery bifurcation) and transfer of the so-called "bad" cholesterol (low-density lipoprotein, LDL) within the multi-layered artery wall. This two-way coupling between the blood flow and corresponding mass transfer of LDL within the artery wall is essential for predictions of regions where atherosclerosis can develop. It is demonstrated that a recently developed mathematical model, which takes into account the complex multi-layer arterial-wall structure, produced LDL profiles within the artery wall in good agreement with in-vivo experiments in rabbits, and it can be used for predictions of locations where the initial stage of development of atherosclerosis may take place. The second example includes a combination of pulsating blood flow and medical drug delivery and deposition controlled by external magnetic field gradients in the patient specific carotid artery bifurcation. The results of numerical simulations are compared with own PIV (Particle Image Velocimetry) and MRI (Magnetic Resonance Imaging) in the PDMS (silicon-based organic polymer) phantom. A very good agreement between simulations and experiments is obtained for different stages of the pulsating cycle. Application of the magnetic drug targeting resulted in an increase of up to ten fold in the efficiency of local deposition of the medical drug at desired locations. Finally, the LES (Large Eddy Simulation) of the aerosol distribution within the human respiratory system that includes up to eight bronchial generations is performed. A very good agreement between simulations and MRV (Magnetic Resonance Velocimetry) measurements is obtained

  6. The NASA-Goddard Multi-Scale Modeling Framework - Land Information System: Global Land/atmosphere Interaction with Resolved Convection

    NASA Technical Reports Server (NTRS)

    Mohr, Karen Irene; Tao, Wei-Kuo; Chern, Jiun-Dar; Kumar, Sujay V.; Peters-Lidard, Christa D.

    2013-01-01

    The present generation of general circulation models (GCM) use parameterized cumulus schemes and run at hydrostatic grid resolutions. To improve the representation of cloud-scale moist processes and landeatmosphere interactions, a global, Multi-scale Modeling Framework (MMF) coupled to the Land Information System (LIS) has been developed at NASA-Goddard Space Flight Center. The MMFeLIS has three components, a finite-volume (fv) GCM (Goddard Earth Observing System Ver. 4, GEOS-4), a 2D cloud-resolving model (Goddard Cumulus Ensemble, GCE), and the LIS, representing the large-scale atmospheric circulation, cloud processes, and land surface processes, respectively. The non-hydrostatic GCE model replaces the single-column cumulus parameterization of fvGCM. The model grid is composed of an array of fvGCM gridcells each with a series of embedded GCE models. A horizontal coupling strategy, GCE4fvGCM4Coupler4LIS, offered significant computational efficiency, with the scalability and I/O capabilities of LIS permitting landeatmosphere interactions at cloud-scale. Global simulations of 2007e2008 and comparisons to observations and reanalysis products were conducted. Using two different versions of the same land surface model but the same initial conditions, divergence in regional, synoptic-scale surface pressure patterns emerged within two weeks. The sensitivity of largescale circulations to land surface model physics revealed significant functional value to using a scalable, multi-model land surface modeling system in global weather and climate prediction.

  7. Aerosol-cloud-precipitation interactions in warm clouds in the PNNL-MMF multi-scale aerosol-climate model

    NASA Astrophysics Data System (ADS)

    Wang, M.; Ghan, S.; Liu, X.; Ovchinnikov, M.; Chand, D.; Qian, Y.; Easter, R. C.; Morrison, H.; Marchand, R.

    2011-12-01

    Aerosol-cloud-precipitation interactions in warm clouds are examined in the multi-scale aerosol-climate model PNNL-MMF, which is an extension of a multi-scale modeling framework (MMF) model. The extended model treats aerosol-cloud-precipitation interactions using a two-moment cloud microphysics scheme in the cloud-resolving model component of the MMF at much finer spatial and temporal scales than in conventional global climate models. The dependence of the probability of precipitation (POP) on liquid water path (LWP) and aerosol loading in the MMF model is in reasonable agreement with the satellite observations. In contrast, the dependence of POP on aerosol loading in a global model with a conventional cloud parameterization (Community Atmosphere Model Version 5, or CAM5) is much stronger than in the MMF and in the satellite observations. The stronger dependence of POP on aerosol loading in CAM5 is consistent with the much larger role played by autoconversion in rain production in CAM5 (48%) than that in the MMF model (3.2%). The better agreement in the dependence of POP on aerosol loading between the MMF model and the satellite observations suggests that the smaller indirect forcing in the MMF is more realistic. Rain susceptibility is further examined to explore how surface rain rate may depend on cloud droplet number concentration (CDNC) and aerosol loading. It is found that the rain susceptibility strongly depends on the relative contribution of autoconversion and accretion in rain production. In tropical marine clouds, surface rain rate is positively correlated with cloud-top droplet effective radius, consistent with satellite observations. However, surface rain rate and column-mean CDNC are not strongly correlated, as the relative contribution of autoconversion is small in these clouds. In mid-latitude marine clouds, autoconversion plays a more important role in rain production in the MMF model, especially at the intermediate LWPs (200-400 g m-2), which

  8. An in silico case study of idiopathic dilated cardiomyopathy via a multi-scale model of the cardiovascular system.

    PubMed

    Bhattacharya-Ghosh, Benjamin; Bozkurt, Selim; Rutten, Marcel C M; van de Vosse, Frans N; Díaz-Zuccarini, Vanessa

    2014-10-01

    Mathematical modelling has been used to comprehend the pathology and the assessment of different treatment techniques such as heart failure and left ventricular assist device therapy in the cardiovascular field. In this study, an in-silico model of the heart is developed to understand the effects of idiopathic dilated cardiomyopathy (IDC) as a pathological scenario, with mechanisms described at the cellular, protein and organ levels. This model includes the right and left atria and ventricles, as well as the systemic and pulmonary arteries and veins. First, a multi-scale model of the whole heart is simulated for healthy conditions. Subsequently, the model is modified at its microscopic and macroscopic spatial scale to obtain the characteristics of IDC. The extracellular calcium concentration, the binding affinity of calcium binding proteins and the maximum and minimum elastances have been identified as key parameters across all relevant scales. The modified parameters cause a change in (a) intracellular calcium concentration characterising cellular properties, such as calcium channel currents or the action potential, (b) the proteins being involved in the sliding filament mechanism and the proportion of the attached crossbridges at the protein level, as well as (c) the pressure and volume values at the organ level. This model allows to obtain insight and understanding of the effects of the treatment techniques, from a physiological and biological point of view. PMID:25147131

  9. Multi-scale damage modelling in a ceramic matrix composite using a finite-element microstructure meshfree methodology.

    PubMed

    Saucedo-Mora, L; Marrow, T J

    2016-07-13

    The problem of multi-scale modelling of damage development in a SiC ceramic fibre-reinforced SiC matrix ceramic composite tube is addressed, with the objective of demonstrating the ability of the finite-element microstructure meshfree (FEMME) model to introduce important aspects of the microstructure into a larger scale model of the component. These are particularly the location, orientation and geometry of significant porosity and the load-carrying capability and quasi-brittle failure behaviour of the fibre tows. The FEMME model uses finite-element and cellular automata layers, connected by a meshfree layer, to efficiently couple the damage in the microstructure with the strain field at the component level. Comparison is made with experimental observations of damage development in an axially loaded composite tube, studied by X-ray computed tomography and digital volume correlation. Recommendations are made for further development of the model to achieve greater fidelity to the microstructure. This article is part of the themed issue 'Multiscale modelling of the structural integrity of composite materials'.

  10. An in silico case study of idiopathic dilated cardiomyopathy via a multi-scale model of the cardiovascular system.

    PubMed

    Bhattacharya-Ghosh, Benjamin; Bozkurt, Selim; Rutten, Marcel C M; van de Vosse, Frans N; Díaz-Zuccarini, Vanessa

    2014-10-01

    Mathematical modelling has been used to comprehend the pathology and the assessment of different treatment techniques such as heart failure and left ventricular assist device therapy in the cardiovascular field. In this study, an in-silico model of the heart is developed to understand the effects of idiopathic dilated cardiomyopathy (IDC) as a pathological scenario, with mechanisms described at the cellular, protein and organ levels. This model includes the right and left atria and ventricles, as well as the systemic and pulmonary arteries and veins. First, a multi-scale model of the whole heart is simulated for healthy conditions. Subsequently, the model is modified at its microscopic and macroscopic spatial scale to obtain the characteristics of IDC. The extracellular calcium concentration, the binding affinity of calcium binding proteins and the maximum and minimum elastances have been identified as key parameters across all relevant scales. The modified parameters cause a change in (a) intracellular calcium concentration characterising cellular properties, such as calcium channel currents or the action potential, (b) the proteins being involved in the sliding filament mechanism and the proportion of the attached crossbridges at the protein level, as well as (c) the pressure and volume values at the organ level. This model allows to obtain insight and understanding of the effects of the treatment techniques, from a physiological and biological point of view.

  11. Multi-scale damage modelling in a ceramic matrix composite using a finite-element microstructure meshfree methodology.

    PubMed

    Saucedo-Mora, L; Marrow, T J

    2016-07-13

    The problem of multi-scale modelling of damage development in a SiC ceramic fibre-reinforced SiC matrix ceramic composite tube is addressed, with the objective of demonstrating the ability of the finite-element microstructure meshfree (FEMME) model to introduce important aspects of the microstructure into a larger scale model of the component. These are particularly the location, orientation and geometry of significant porosity and the load-carrying capability and quasi-brittle failure behaviour of the fibre tows. The FEMME model uses finite-element and cellular automata layers, connected by a meshfree layer, to efficiently couple the damage in the microstructure with the strain field at the component level. Comparison is made with experimental observations of damage development in an axially loaded composite tube, studied by X-ray computed tomography and digital volume correlation. Recommendations are made for further development of the model to achieve greater fidelity to the microstructure. This article is part of the themed issue 'Multiscale modelling of the structural integrity of composite materials'. PMID:27242308

  12. A Micromechanical Unit Cell Model of 2 × 2 Twill Woven Fabric Textile Composite for Multi Scale Analysis

    NASA Astrophysics Data System (ADS)

    Dixit, A.; Mali, H. S.; Misra, R. K.

    2014-04-01

    Woven fabric based composite materials are being considered for potential structural applications in automotive and aircraft industries due to their better out of plane strength, stiffness and toughness properties than ordinary composite laminates. This paper presents the micromechanical unit cell model of 2 × 2 twill woven fabric textile composite for the estimation of in-plane elastic properties. Modelling of unit cell and its analysis for this new model is developed by using open source coded tool TexGen and finite element software, ABAQUS® respectively. The predicted values are in good agreement with the experimental results reported in literature. To ascertain the effectiveness of the developed model parametric studies have also been conducted on the predicted elastic properties in order to investigate the effects of various geometric parameters such as yarn spacing, fabric thickness, yarn width and fibre volume fraction. The scope of altering weave pattern and yarn characteristics is facilitated in this developed model. Further this model can be implemented for the multi-scale micro/macro-mechanical analysis for the calculation of strength and stiffness of laminates structure made of 2 × 2 twill composite.

  13. Impact of spatial data resolution on simulated catchment water balances and model performance of the multi-scale TOPLATS model

    NASA Astrophysics Data System (ADS)

    Bormann, H.

    2005-10-01

    This paper analyses the effect of spatial input data resolution on the simulated water balances and flow components using the multi-scale hydrological model TOPLATS. A data set of 25m resolution of the central German Dill catchment (693 km2 is used for investigation. After an aggregation of digital elevation model, soil map and land use classification to 50 m, 75 m, 100 m, 150 m, 200 m, 300 m, 500 m, 1000 m and 2000 m, water balances and water flow components are calculated for the entire Dill catchment as well as for 3 subcatchments without any recalibration. The study shows that both model performance measures as well as simulated water balances almost remain constant for most of the aggregation steps for all investigated catchments. Slight differences occur for single catchments at the resolution of 50-500 m (e.g. 0-3% for annual stream flow), significant differences at the resolution of 1000 m and 2000 m (e.g. 2-12% for annual stream flow). These differences can be explained by the fact that the statistics of certain input data (land use data in particular as well as soil physical characteristics) changes significantly at these spatial resolutions, too. The impact of smoothing the relief by aggregation occurs continuously but is not reflected by the simulation results. To study the effect of aggregation of land use data in detail, three different land use scenarios are aggregated which were generated aiming on economic optimisation at different field sizes (0.5 ha, 1.5 ha and 5.0 ha). The changes induced by aggregation of these land use scenarios are comparable with respect to catchment water balances compared to the current land use. A correlation analysis only in some cases reveals high correlation between changes in both input data and in simulation results for all catchments and land use scenarios combinations (e.g. evapotranspiration is correlated to land use, runoff generation is correlated to soil properties). Predominantly the correlation between

  14. Hierarchical multi-scale approach to validation and uncertainty quantification of hyper-spectral image modeling

    NASA Astrophysics Data System (ADS)

    Engel, Dave W.; Reichardt, Thomas A.; Kulp, Thomas J.; Graff, David L.; Thompson, Sandra E.

    2016-05-01

    Validating predictive models and quantifying uncertainties inherent in the modeling process is a critical component of the HARD Solids Venture program [1]. Our current research focuses on validating physics-based models predicting the optical properties of solid materials for arbitrary surface morphologies and characterizing the uncertainties in these models. We employ a systematic and hierarchical approach by designing physical experiments and comparing the experimental results with the outputs of computational predictive models. We illustrate this approach through an example comparing a micro-scale forward model to an idealized solid-material system and then propagating the results through a system model to the sensor level. Our efforts should enhance detection reliability of the hyper-spectral imaging technique and the confidence in model utilization and model outputs by users and stakeholders.

  15. Pore Scale and Continuum Modeling for Gas Flow Pattern obtained by Multi-Scale Optical Imaging Technique

    NASA Astrophysics Data System (ADS)

    Lazik, D.; Samani, S.; Geistlinger, H.

    2008-12-01

    A multi-scale optical imaging technique was developed allowing for the 2D observation of two phase flow in porous media at two different scales simultaneously: Using two coupled camera systems a 2D flow cell (0.5 x 0.5 m²) is recorded entirely at the bench scale and at the pore scale with a spatial resolution of 0.5 mm and 0.01 mm respectively. The technique is applied to study channelized gas flow in saturated 0.5mm glass beads. We analyze the phase distribution at the pore scale and derive a pixel-based method for the measurement of saturation at the larger scale. Pore-Scale-Models: Both a grain-size- and flow rate-dependent transition are observed in the gas flow pattern. Standard quasi-static criteria do not explain the experimental results, since they do not take into account the competition between stabilizing friction forces and destabilizing capillary and gravitational forces. Conceptualizing the steady state tortuous gas flow as core-annular flow and applying Hagen-Poiseuille flow for a straight capillary, we propose a flow rate and grain-size-dependent stability criterion (coherence condition) that accounts for the experimental results. Continuum Scale Models: The main objective of this paper is to test the validity of the continuum approach for two-fluid flow for macroscopic homogeneous media. Using a reasonable log-normal distribution of capillary radii that led to a matrix potential that fits the experimental steady-state capillary pressure, the continuum model (TOUGH2) was able to describe the functional form of the dynamical gas volume, an integral flow property, as a function of the flow rate for the 0.5mm glass beads. On the other hand, the continuum model fails to describe the spatial-temporal distribution of the gas flow. For the first time, we were able to quantify the plateau-like gas distribution using optical tomography. This result is in strong contradiction to the Gaussian-like distribution obtained from the continuum model. Both

  16. Interacting price model and fluctuation behavior analysis from Lempel-Ziv complexity and multi-scale weighted-permutation entropy

    NASA Astrophysics Data System (ADS)

    Li, Rui; Wang, Jun

    2016-01-01

    A financial price model is developed based on the voter interacting system in this work. The Lempel-Ziv complexity is introduced to analyze the complex behaviors of the stock market. Some stock market stylized facts including fat tails, absence of autocorrelation and volatility clustering are investigated for the proposed price model firstly. Then the complexity of fluctuation behaviors of the real stock markets and the proposed price model are mainly explored by Lempel-Ziv complexity (LZC) analysis and multi-scale weighted-permutation entropy (MWPE) analysis. A series of LZC analyses of the returns and the absolute returns of daily closing prices and moving average prices are performed. Moreover, the complexity of the returns, the absolute returns and their corresponding intrinsic mode functions (IMFs) derived from the empirical mode decomposition (EMD) with MWPE is also investigated. The numerical empirical study shows similar statistical and complex behaviors between the proposed price model and the real stock markets, which exhibits that the proposed model is feasible to some extent.

  17. HPC Aspects of Variable-Resolution Global Climate Modeling using a Multi-scale Convection Parameterization

    EPA Science Inventory

    High performance computing (HPC) requirements for the new generation variable grid resolution (VGR) global climate models differ from that of traditional global models. A VGR global model with 15 km grids over the CONUS stretching to 60 km grids elsewhere will have about ~2.5 tim...

  18. The North American Carbon Program Multi-scale synthesis and Terrestrial Model Intercomparison Project Part 1: Overview and experimental design

    SciTech Connect

    Huntzinger, D.N.; Schwalm, C.; Michalak, A.M; Schaefer, K.; King, A.W.; Wei, Y.; Jacobson, A.; Liu, S.; Cook, R.; Post, W.M.; Berthier, G.; Hayes, D.; Huang, M.; Ito, A.; Lei, H.; Lu, C.; Mao, J.; Peng, C.H.; Peng, S.; Poulter, B.; Riccuito, D.; Shi, X.; Tian, H.; Wang, W.; Zeng, N.; Zhao, F.; Zhu, Q.

    2013-01-01

    Terrestrial biosphere models (TBMs) have become an integral tool for extrapolating local observations and understanding of land-atmosphere carbon exchange to larger regions. The North American Carbon Program (NACP) Multi-scale synthesis and Terrestrial Model Intercomparison Project (MsTMIP) is a formal model intercomparison and evaluation effort focused on improving the diagnosis and attribution of carbon exchange at regional and global scales. MsTMIP builds upon current and past synthesis activities, and has a unique framework designed to isolate, interpret, and inform understanding of how model structural differences impact estimates of carbon uptake and release. Here we provide an overview of the MsTMIP effort and describe how the MsTMIP experimental design enables the assessment and quantification of TBM structural uncertainty. Model structure refers to the types of processes considered (e.g. nutrient cycling, disturbance, lateral transport of carbon), and how these processes are represented (e.g. photosynthetic formulation, temperature sensitivity, respiration) in the models. By prescribing a common experimental protocol with standard spin-up procedures and driver data sets, we isolate any biases and variability in TBM estimates of regional and global carbon budgets resulting from differences in the models themselves (i.e. model structure) and model-specific parameter values. An initial intercomparison of model structural differences is represented using hierarchical cluster diagrams (a.k.a. dendrograms), which highlight similarities and differences in how models account for carbon cycle, vegetation, energy, and nitrogen cycle dynamics. We show that, despite the standardized protocol used to derive initial conditions, models show a high degree of variation for GPP, total living biomass, and total soil carbon, underscoring the influence of differences in model structure and parameterization on model estimates.

  19. A framework for integrated, multi-scale model construction and uncertainty assessment

    NASA Astrophysics Data System (ADS)

    Schmitz, Oliver; de Kok, Jean-Luc; de Jong, Kor; Karssenberg, Derek

    2015-04-01

    The component-based software development practice promotes the construction of self-contained modules with defined input and output interfaces. In environmental modelling, we can adopt this development practice to construct more generic, reusable component models. Here, modellers need to implement a state transition function to describe a specific environmental process, and to specify the required external inputs and parameters to simulate the change of real-world processes over time. Depending on the usage of a component model, such as standalone execution or as part of an integrated model, the source of the external input needs to be specified. The required external inputs can thereby be obtained from disk by a file operation in case of a standalone execution; or inputs can be obtained from other component models, when the component model is used in an integrated model. Using different notations to specify input requirements, however, requires a modification of the state transition function per application case of a component model and therefore would reduce its generic nature. We propose the function object notation as a means to specify input sources of a component model and as a uniform syntax to express input requirements. At component initialisation, the function objects can be parametrised with different external sources. In addition to a uniform syntax, the function object notation allows modellers to specify a request-reply execution flow of the coupled models. We extended the request-reply execution approach to allow for Monte Carlo simulations, and implemented a software framework prototype in Python using the PCRaster module (http://www.pcraster.eu) for field-based modelling. We demonstrate the usage of the framework by building an exemplary integrated model by coupling components simulating land use change, hydrology and eucalyptus tree growth at different temporal discretisations to obtain the probability for bioenergy plantations in a hypothetical

  20. Investigation of the impacts of Asian pollution on Pacific storm track using multi-scale modeling results

    NASA Astrophysics Data System (ADS)

    Wang, Y.; Wang, M.; Ghan, S. J.; Zhang, R.

    2012-12-01

    Long-term satellite data and numerical simulations with the cloud-resolving model (CRM) suggest that increasing pollution levels in Asia and associated outflows may impact the Pacific storm track by altering cloud development, lifetime, albedo, and precipitation. In this study, results from a pair of 6-year global atmosphere simulations were analyzed, using the multi-scale aerosol-climate model PNNL-MMF where a CRM is embedded within each grid column of the Community Atmosphere Model (CAM). Two different aerosol conditions are considered in the simulations, representing Present Day (PD) and Pre-Industrial (PI) emissions, respectively. A comparison of those two scenarios shows that over the Northwest Pacific region aerosol optical depth is increased by 50% and cloud droplet number concentration is doubled under the influence of Asian pollution outflow. Meanwhile, cloud liquid water path and ice water path are enhanced by 9% and 8% due to the elevated aerosol loading in the PD case. The larger percentage of convective cloud coverage and the higher cloud top height in the PD case demonstrate that the convection strength of mid-latitude cyclones is invigorated. A 3% increase of precipitation induced by the larger PD aerosol concentration is found over the Northwest Pacific area. Smaller cloud droplets and the larger liquid and ice water path lead to the increase of cloud optical thickness by 10% in the PD case. Cloud shortwave and longwave forcing at the top of atmosphere (TOA) are enlarged by 7% and 6%, respectively. The poleward eddy heat transport along the storm track at 850 hPa is enhanced by 5% in the PD case. In addition, the results from the standard CAM model (no embedded CRM), simulates a similar increase in the aerosol concentration in the PD case but predicts significant suppression of the convection strength and heavy precipitation associated with the cyclones. This indicates that the multi-scale framework approach is critical for reproducing the aerosol

  1. Probing red blood cell mechanics, rheology and dynamics with a two-component multi-scale model

    PubMed Central

    Li, Xuejin; Peng, Zhangli; Lei, Huan; Dao, Ming; Karniadakis, George Em

    2014-01-01

    This study is partially motivated by the validation of a new two-component multi-scale cell model we developed recently that treats the lipid bilayer and the cytoskeleton as two distinct components. Here, the whole cell model is validated and compared against several available experiments that examine red blood cell (RBC) mechanics, rheology and dynamics. First, we investigated RBC deformability in a microfluidic channel with a very small cross-sectional area and quantified the mechanical properties of the RBC membrane. Second, we simulated twisting torque cytometry and compared predicted rheological properties of the RBC membrane with experimental measurements. Finally, we modelled the tank-treading (TT) motion of a RBC in a shear flow and explored the effect of channel width variation on the TT frequency. We also investigated the effects of bilayer–cytoskeletal interactions on these experiments and our simulations clearly indicated that they play key roles in the determination of cell membrane mechanical, rheological and dynamical properties. These simulations serve as validation tests and moreover reveal the capabilities and limitations of the new whole cell model. PMID:24982252

  2. Three-dimensional multi-scale model of deformable platelets adhesion to vessel wall in blood flow

    PubMed Central

    Wu, Ziheng; Xu, Zhiliang; Kim, Oleg; Alber, Mark

    2014-01-01

    When a blood vessel ruptures or gets inflamed, the human body responds by rapidly forming a clot to restrict the loss of blood. Platelets aggregation at the injury site of the blood vessel occurring via platelet–platelet adhesion, tethering and rolling on the injured endothelium is a critical initial step in blood clot formation. A novel three-dimensional multi-scale model is introduced and used in this paper to simulate receptor-mediated adhesion of deformable platelets at the site of vascular injury under different shear rates of blood flow. The novelty of the model is based on a new approach of coupling submodels at three biological scales crucial for the early clot formation: novel hybrid cell membrane submodel to represent physiological elastic properties of a platelet, stochastic receptor–ligand binding submodel to describe cell adhesion kinetics and lattice Boltzmann submodel for simulating blood flow. The model implementation on the GPU cluster significantly improved simulation performance. Predictive model simulations revealed that platelet deformation, interactions between platelets in the vicinity of the vessel wall as well as the number of functional GPIbα platelet receptors played significant roles in platelet adhesion to the injury site. Variation of the number of functional GPIbα platelet receptors as well as changes of platelet stiffness can represent effects of specific drugs reducing or enhancing platelet activity. Therefore, predictive simulations can improve the search for new drug targets and help to make treatment of thrombosis patient-specific. PMID:24982253

  3. Probing red blood cell mechanics, rheology and dynamics with a two-component multi-scale model.

    PubMed

    Li, Xuejin; Peng, Zhangli; Lei, Huan; Dao, Ming; Karniadakis, George Em

    2014-08-01

    This study is partially motivated by the validation of a new two-component multi-scale cell model we developed recently that treats the lipid bilayer and the cytoskeleton as two distinct components. Here, the whole cell model is validated and compared against several available experiments that examine red blood cell (RBC) mechanics, rheology and dynamics. First, we investigated RBC deformability in a microfluidic channel with a very small cross-sectional area and quantified the mechanical properties of the RBC membrane. Second, we simulated twisting torque cytometry and compared predicted rheological properties of the RBC membrane with experimental measurements. Finally, we modelled the tank-treading (TT) motion of a RBC in a shear flow and explored the effect of channel width variation on the TT frequency. We also investigated the effects of bilayer-cytoskeletal interactions on these experiments and our simulations clearly indicated that they play key roles in the determination of cell membrane mechanical, rheological and dynamical properties. These simulations serve as validation tests and moreover reveal the capabilities and limitations of the new whole cell model.

  4. Multi scale modeling of the elastic properties of polymer-clay nanocomposites

    NASA Astrophysics Data System (ADS)

    Pahlavan Pour, Maryam

    Polymer-Clay Nanocomposites (PCN) are known to improve the mechanical properties of bulk polymers, even for modest clay loadings. This enhancement is due to the high aspect ratio and mechanical properties of the nanoclay platelets. Additionally, the interphase zone created by altered polymer chains in the vicinity of the nanoclays plays an important reinforcing role. Several analytical approaches exist for predicting the elastic properties of PCN, ranging from simplified two-step models to more complex one-step methods. However, no thorough study has yet rigorously verified the accuracy of these models. On the other hand, the numerical models that are commonly used to evaluate the analytical models are still far from modeling the real PCN microstructure reported in the literature. For example, most of the models have failed to model the detailed 3D microstructure considering randomly positioned reinforcing particles, the large nanoclay aspect ratio and the explicit incorporation of the constituent phases. More significantly, most of numerical studies have been reported without a thorough determination of the appropriate Representative Volume Element (RVE) due its computational burden, resulting in benchmark results of questionable accuracy. The main purpose of this thesis was to evaluate the accuracy of homogenization models for predicting the mechanical behavior of nanoclay nanocomposites. First, the validity of commonly used analytical micromechanical models for the prediction of exfoliated PCN elastic properties was evaluated with the help of 3D Finite Element (FE) simulations. In particular, special attention was devoted to the interphase around the nanoclays. The modeling strategy was a two-step procedure relying on the Effective Particle (EP) concept, in which the multi-layer reinforcing stacks were replaced by homogenized particles. The accuracy of the numerical models was guaranteed, within a given tolerance, by rigorous determination of the RVE. It was

  5. Multi-scale problem in the model of RNA virus evolution

    NASA Astrophysics Data System (ADS)

    Korobeinikov, Andrei; Archibasov, Aleksei; Sobolev, Vladimir

    2016-06-01

    A mathematical or computational model in evolutionary biology should necessary combine several comparatively fast processes, which actually drive natural selection and evolution, with a very slow process of evolution. As a result, several very different time scales are simultaneously present in the model; this makes its analytical study an extremely difficult task. However, the significant difference of the time scales implies the existence of a possibility of the model order reduction through a process of time separation. In this paper we conduct the procedure of model order reduction for a reasonably simple model of RNA virus evolution reducing the original system of three integro-partial derivative equations to a single equation. Computations confirm that there is a good fit between the results for the original and reduced models.

  6. Quantification of structural uncertainties in multi-scale models; case study of the Lublin Basin, Poland

    NASA Astrophysics Data System (ADS)

    Małolepszy, Zbigniew; Szynkaruk, Ewa

    2015-04-01

    The multiscale static modeling of regional structure of the Lublin Basin is carried on in the Polish Geological Institute, in accordance with principles of integrated 3D geological modelling. The model is based on all available geospatial data from Polish digital databases and analogue archives. Mapped regional structure covers the area of 260x80 km located between Warsaw and Polish-Ukrainian border, along NW-SE-trending margin of the East European Craton. Within the basin, the Paleozoic beds with coalbearing Carboniferous and older formations containing hydrocarbons and unconventional prospects are covered unconformably by Permo-Mesozoic and younger rocks. Vertical extent of the regional model is set from topographic surface to 6000 m ssl and at the bottom includes some Proterozoic crystalline formations of the craton. The project focuses on internal consistency of the models built at different scales - from basin (small) scale to field-scale (large-scale). The models, nested in the common structural framework, are being constructed with regional geological knowledge, ensuring smooth transition in the 3D model resolution and amount of geological detail. Major challenge of the multiscale approach to subsurface modelling is the assessment and consistent quantification of various types of geological uncertainties tied to those various scale sub-models. Decreasing amount of information with depth and, particularly, very limited data collected below exploration targets, as well as accuracy and quality of data, all have the most critical impact on the modelled structure. In deeper levels of the Lublin Basin model, seismic interpretation of 2D surveys is sparsely tied to well data. Therefore time-to-depth conversion carries one of the major uncertainties in the modeling of structures, especially below 3000 m ssl. Furthermore, as all models at different scales are based on the same dataset, we must deal with different levels of generalization of geological structures. The

  7. The Radiative Properties of Small Clouds: Multi-Scale Observations and Modeling

    SciTech Connect

    Feingold, Graham; McComiskey, Allison

    2013-09-25

    Warm, liquid clouds and their representation in climate models continue to represent one of the most significant unknowns in climate sensitivity and climate change. Our project combines ARM observations, LES modeling, and satellite imagery to characterize shallow clouds and the role of aerosol in modifying their radiative effects.

  8. Adaptive Remodeling of Achilles Tendon: A Multi-scale Computational Model

    PubMed Central

    Rubenson, Jonas; Umberger, Brian

    2016-01-01

    While it is known that musculotendon units adapt to their load environments, there is only a limited understanding of tendon adaptation in vivo. Here we develop a computational model of tendon remodeling based on the premise that mechanical damage and tenocyte-mediated tendon damage and repair processes modify the distribution of its collagen fiber lengths. We explain how these processes enable the tendon to geometrically adapt to its load conditions. Based on known biological processes, mechanical and strain-dependent proteolytic fiber damage are incorporated into our tendon model. Using a stochastic model of fiber repair, it is assumed that mechanically damaged fibers are repaired longer, whereas proteolytically damaged fibers are repaired shorter, relative to their pre-damage length. To study adaptation of tendon properties to applied load, our model musculotendon unit is a simplified three-component Hill-type model of the human Achilles-soleus unit. Our model results demonstrate that the geometric equilibrium state of the Achilles tendon can coincide with minimization of the total metabolic cost of muscle activation. The proposed tendon model independently predicts rates of collagen fiber turnover that are in general agreement with in vivo experimental measurements. While the computational model here only represents a first step in a new approach to understanding the complex process of tendon remodeling in vivo, given these findings, it appears likely that the proposed framework may itself provide a useful theoretical foundation for developing valuable qualitative and quantitative insights into tendon physiology and pathology. PMID:27684554

  9. Multi-scale analysis of a household level agent-based model of landcover change.

    PubMed

    Evans, Tom P; Kelley, Hugh

    2004-08-01

    Scale issues have significant implications for the analysis of social and biophysical processes in complex systems. These same scale implications are likewise considerations for the design and application of models of landcover change. Scale issues have wide-ranging effects from the representativeness of data used to validate models to aggregation errors introduced in the model structure. This paper presents an analysis of how scale issues affect an agent-based model (ABM) of landcover change developed for a research area in the Midwest, USA. The research presented here explores how scale factors affect the design and application of agent-based landcover change models. The ABM is composed of a series of heterogeneous agents who make landuse decisions on a portfolio of cells in a raster-based programming environment. The model is calibrated using measures of fit derived from both spatial composition and spatial pattern metrics from multi-temporal landcover data interpreted from historical aerial photography. A model calibration process is used to find a best-fit set of parameter weights assigned to agents' preferences for different landuses (agriculture, pasture, timber production, and non-harvested forest). Previous research using this model has shown how a heterogeneous set of agents with differing preferences for a portfolio of landuses produces the best fit to landcover changes observed in the study area. The scale dependence of the model is explored by varying the resolution of the input data used to calibrate the model (observed landcover), ancillary datasets that affect land suitability (topography), and the resolution of the model landscape on which agents make decisions. To explore the impact of these scale relationships the model is run with input datasets constructed at the following spatial resolutions: 60, 90, 120, 150, 240, 300 and 480 m. The results show that the distribution of landuse-preference weights differs as a function of scale. In addition

  10. A Robust Multi-Scale Modeling System for the Study of Cloud and Precipitation Processes

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo

    2012-01-01

    During the past decade, numerical weather and global non-hydrostatic models have started using more complex microphysical schemes originally developed for high resolution cloud resolving models (CRMs) with 1-2 km or less horizontal resolutions. These microphysical schemes affect the dynamic through the release of latent heat (buoyancy loading and pressure gradient) the radiation through the cloud coverage (vertical distribution of cloud species), and surface processes through rainfall (both amount and intensity). Recently, several major improvements of ice microphysical processes (or schemes) have been developed for cloud-resolving model (Goddard Cumulus Ensemble, GCE, model) and regional scale (Weather Research and Forecast, WRF) model. These improvements include an improved 3-ICE (cloud ice, snow and graupel) scheme (Lang et al. 2010); a 4-ICE (cloud ice, snow, graupel and hail) scheme and a spectral bin microphysics scheme and two different two-moment microphysics schemes. The performance of these schemes has been evaluated by using observational data from TRMM and other major field campaigns. In this talk, we will present the high-resolution (1 km) GeE and WRF model simulations and compared the simulated model results with observation from recent field campaigns [i.e., midlatitude continental spring season (MC3E; 2010), high latitude cold-season (C3VP, 2007; GCPEx, 2012), and tropical oceanic (TWP-ICE, 2006)].

  11. Determinants of wood thrush nest success: A multi-scale, model selection approach

    USGS Publications Warehouse

    Driscoll, M.J.L.; Donovan, T.; Mickey, R.; Howard, A.; Fleming, K.K.

    2005-01-01

    We collected data on 212 wood thrush (Hylocichla mustelina) nests in central New York from 1998 to 2000 to determine the factors that most strongly influence nest success. We used an information-theoretic approach to assess and rank 9 models that examined the relationship between nest success (i.e., the probability that a nest would successfully fledge at least 1 wood thrush offspring) and habitat conditions at different spatial scales. We found that 4 variables were significant predictors of nesting success for wood thrushes: (1) total core habitat within 5 km of a study site, (2) distance to forest-field edge, (3) total forest cover within 5 km of the study site, and (4) density and variation in diameter of trees and shrubs surrounding the nest. The coefficients of these predictors were all positive. Of the 9 models evaluated, amount of core habitat in the 5-km landscape was the best-fit model, but the vegetation structure model (i.e., the density of trees and stems surrounding a nest) was also supported by the data. Based on AIC weights, enhancement of core area is likely to be a more effective management option than any other habitat-management options explored in this study. Bootstrap analysis generally confirmed these results; core and vegetation structure models were ranked 1, 2, or 3 in over 50% of 1,000 bootstrap trials. However, bootstrap results did not point to a decisive model, which suggests that multiple habitat factors are influencing wood thrush nesting success. Due to model uncertainty, we used a model averaging approach to predict the success or failure of each nest in our dataset. This averaged model was able to correctly predict 61.1% of nest outcomes.

  12. Multi-scale modeling for the self-assembly of DNA-functionalized nanoparticle into supperlattice and Wulff polydedra

    NASA Astrophysics Data System (ADS)

    Li, Ting; Auyeung, Evelyn; Mirkin, Chad; Olvera de La Cruz, Monica; Northwestern University Team

    2014-03-01

    Since 1996, DNA hybridization has proven robust for programmable self-assembly of nanoparticles (NPs). Recently, we showed that through a ``slow cooling'' method, DNA functionalized nanospheres or so-called ``programmable atom equivalents'' can assemble into crystals with a specific and uniform habit. Here we perform molecular dynamics simulations on multi-scale models to study and predict the corresponding shapes. Firstly, we use a scale-accurate coarse-grained model with explicit DNA chains to estimate surface energy ratios for different surface orientations, and predict the corresponding Wulff polyhedra based on these values. Secondly, we use a colloidal model in which each DNA coated nanosphere is represented by a single bead to simulate the growth dynamics of the crystals. By this method, we confirm the shape for the body-centered-cubic system to be a (110)-enclosed rhombic dodecahedron. But the face-centered-cubic system does not show any uniform shape yet except triangular features with (111) and (100) facets due to crystallographic defects including twinning and stacking faults. These simulated crystal shapes agrees very well with experiments. Air Force Office of Scientific Research (AFOSR) Multidisciplinary University Research Initiative (MURI) FA9550-11-1-0275.

  13. Application of crowd-sourced data to multi-scale evolutionary exposure and vulnerability models

    NASA Astrophysics Data System (ADS)

    Pittore, Massimiliano

    2016-04-01

    Seismic exposure, defined as the assets (population, buildings, infrastructure) exposed to earthquake hazard and susceptible to damage, is a critical -but often neglected- component of seismic risk assessment. This partly stems from the burden associated with the compilation of a useful and reliable model over wide spatial areas. While detailed engineering data have still to be collected in order to constrain exposure and vulnerability models, the availability of increasingly large crowd-sourced datasets (e. g. OpenStreetMap) opens up the exciting possibility to generate incrementally evolving models. Integrating crowd-sourced and authoritative data using statistical learning methodologies can reduce models uncertainties and also provide additional drive and motivation to volunteered geoinformation collection. A case study in Central Asia will be presented and discussed.

  14. Multi-Scale Modeling of Tissues Using CompuCell3D

    PubMed Central

    Swat, Maciej H.; Thomas, Gilberto L.; Belmonte, Julio M.; Shirinifard, Abbas; Hmeljak, Dimitrij; Glazier, James A.

    2013-01-01

    The study of how cells interact to produce tissue development, homeostasis, or diseases was, until recently, almost purely experimental. Now, multi-cell computer simulation methods, ranging from relatively simple cellular automata to complex immersed-boundary and finite-element mechanistic models, allow in silico study of multi-cell phenomena at the tissue scale based on biologically observed cell behaviors and interactions such as movement, adhesion, growth, death, mitosis, secretion of chemicals, chemotaxis, etc. This tutorial introduces the lattice-based Glazier–Graner–Hogeweg (GGH) Monte Carlo multi-cell modeling and the open-source GGH-based CompuCell3D simulation environment that allows rapid and intuitive modeling and simulation of cellular and multi-cellular behaviors in the context of tissue formation and subsequent dynamics. We also present a walkthrough of four biological models and their associated simulations that demonstrate the capabilities of the GGH and CompuCell3D. PMID:22482955

  15. The Sub-Arctic Carbon Cycle: Assimilating Multi-Scale Chamber, Tower and Aircraft Flux Observations into Ecological Models

    NASA Astrophysics Data System (ADS)

    Hill, T. C.; Stoy, P. C.; Baxter, R.; Clement, R.; Disney, M.; Evans, J.; Fletcher, B.; Gornall, J.; Harding, R.; Hartley, I. P.; Ineson, P.; Moncrieff, J.; Phoenix, G.; Sloan, V.; Poyatos, R.; Prieto-Blanco, A.; Subke, J.; Street, L.; Wade, T. J.; Wayolle, A.; Wookey, P.; Williams, M. D.

    2009-12-01

    source/sink status of the landscapes, but cold season data were successfully collected. Aircraft flux measurements during the peak growing season provided an estimate of landscape variability alongside the temporal sampling from fixed tower systems, and a means to constrain upscaling via models. Assimilation of these multi-scale data into an ecosystem carbon model yielded improved constraints on processes, particularly the turnover rates of soil carbon. Our work shows that these improvements cannot be attained with a single source of data (chamber, tower or aircraft).

  16. Design strategies for human & earth systems modeling to meet emerging multi-scale decision support needs

    NASA Astrophysics Data System (ADS)

    Spak, S.; Pooley, M.

    2012-12-01

    The next generation of coupled human and earth systems models promises immense potential and grand challenges as they transition toward new roles as core tools for defining and living within planetary boundaries. New frontiers in community model development include not only computational, organizational, and geophysical process questions, but also the twin objectives of more meaningfully integrating the human dimension and extending applicability to informing policy decisions on a range of new and interconnected issues. We approach these challenges by posing key policy questions that require more comprehensive coupled human and geophysical models, identify necessary model and organizational processes and outputs, and work backwards to determine design criteria in response to these needs. We find that modular community earth system model design must: * seamlessly scale in space (global to urban) and time (nowcasting to paleo-studies) and fully coupled on all component systems * automatically differentiate to provide complete coupled forward and adjoint models for sensitivity studies, optimization applications, and 4DVAR assimilation across Earth and human observing systems * incorporate diagnostic tools to quantify uncertainty in couplings, and in how human activity affects them * integrate accessible community development and application with JIT-compilation, cloud computing, game-oriented interfaces, and crowd-sourced problem-solving We outline accessible near-term objectives toward these goals, and describe attempts to incorporate these design objectives in recent pilot activities using atmosphere-land-ocean-biosphere-human models (WRF-Chem, IBIS, UrbanSim) at urban and regional scales for policy applications in climate, energy, and air quality.

  17. Multi-scale modeling of multi-component reactive transport in geothermal aquifers

    NASA Astrophysics Data System (ADS)

    Nick, Hamidreza M.; Raoof, Amir; Wolf, Karl-Heinz; Bruhn, David

    2014-05-01

    In deep geothermal systems heat and chemical stresses can cause physical alterations, which may have a significant effect on flow and reaction rates. As a consequence it will lead to changes in permeability and porosity of the formations due to mineral precipitation and dissolution. Large-scale modeling of reactive transport in such systems is still challenging. A large area of uncertainty is the way in which the pore-scale information controlling the flow and reaction will behave at a larger scale. A possible choice is to use constitutive relationships relating, for example the permeability and porosity evolutions to the change in the pore geometry. While determining such relationships through laboratory experiments may be limited, pore-network modeling provides an alternative solution. In this work, we introduce a new workflow in which a hybrid Finite-Element Finite-Volume method [1,2] and a pore network modeling approach [3] are employed. Using the pore-scale model, relevant constitutive relations are developed. These relations are then embedded in the continuum-scale model. This approach enables us to study non-isothermal reactive transport in porous media while accounting for micro-scale features under realistic conditions. The performance and applicability of the proposed model is explored for different flow and reaction regimes. References: 1. Matthäi, S.K., et al.: Simulation of solute transport through fractured rock: a higher-order accurate finite-element finite-volume method permitting large time steps. Transport in porous media 83.2 (2010): 289-318. 2. Nick, H.M., et al.: Reactive dispersive contaminant transport in coastal aquifers: Numerical simulation of a reactive Henry problem. Journal of contaminant hydrology 145 (2012), 90-104. 3. Raoof A., et al.: PoreFlow: A Complex pore-network model for simulation of reactive transport in variably saturated porous media, Computers & Geosciences, 61, (2013), 160-174.

  18. Multi-scale Model Coupling for CFD Simulations of Discharge Dispersion in the Sea

    NASA Astrophysics Data System (ADS)

    Robinson, D.; Wood, M.; Piggott, M. D.; Gorman, G.

    2014-12-01

    The processes that influence the dispersion of effluent discharges in the sea occur over a wide range of length and time scales. The distance that effluent can travel before it is considered mixed can be several kilometres, whereas the turbulent eddies that affect the near-field mixing of a discharge can be as small as a few centimetres. The range of scales that are involved mean that it is not generally practical to include all influencing physical phenomena within one model. Typically, the modelling of effluent dispersion is performed using two separate numerical models: a local model of the outlet(s), including the near-field effects of momentum, buoyancy and turbulence; and a larger scale model that can include the far-field effects of tidal-, wind- and wave-driven-currents, water depth variations, atmospheric fluxes, and Coriolis forces. The boundary between the two models is often not strictly defined, but is usually placed at the transition from where the behaviour of the effluent is dominated by the ambient environment, rather than the discharge characteristics and outfall configuration. In most real applications, this transition line varies considerably in time and space. This paper presents the findings of collaborative research between the Applied Modelling and Computation Group (AMCG) at Imperial College London, UK, and HR Wallingford Ltd. Results are presented using a range of coupling methods to link the near- and far-field mixing regions. An idealised domain and tidal conditions are used, with the outfall and ambient conditions typical of those found at small coastal desalination plants. Open-source CFD code Fluidity is used for both the near-field and far-field modelling. Fluidity scales well when run in parallel on large numbers of cores. It also has an anisotropic adaptive mesh capability which allows local control over solution accuracy throughout the domain. This combination means that accuracy can be achieved without excessive time costs, with

  19. Influence of different mechanical stimuli in a multi-scale mechanobiological isotropic model for bone remodelling.

    PubMed

    Mercuri, E G F; Daniel, A L; Hecke, M B; Carvalho, L

    2016-09-01

    This work represents a study of a mathematical model that describes the biological response to different mechanical stimuli in a cellular dynamics model for bone remodelling. The biological system discussed herein consists of three specialised cellular types, responsive osteoblasts, active osteoblasts and osteoclasts, three types of signalling molecules, transforming growth factor beta (TGF-β), receptor activator of nuclear factor kappa-b ligand (RANKL) and osteoprotegerin (OPG) and the parathyroid hormone (PTH). Three proposals for mechanical stimuli were tested: strain energy density (SED), hydrostatic and deviatoric parts of SED. The model was tested in a two-dimensional geometry of a standard human femur. The spatial discretization was performed by the finite element method while the temporal evolution of the variables was calculated by the 4th order Runge-Kutta method. The obtained results represent the temporal evolution of the apparent density distribution and the mean apparent density and thickness for the cortical bone after 600 days of remodelling simulation. The main contributions of this paper are the coupling of mechanical and biological models and the exploration of how the different mechanical stimuli affect the cellular activity in different types of physical activities. The results revealed that hydrostatic SED stimulus was able to form more cortical bone than deviatoric SED and total SED stimuli. The computational model confirms how different mechanical stimuli can impact in the balance of bone homeostasis.

  20. Accessible, almost ab initio multi-scale modeling of entangled polymers via slip-links

    NASA Astrophysics Data System (ADS)

    Andreev, Marat

    It is widely accepted that dynamics of entangled polymers can be described by the tube model. Here we advocate for an alternative approach to entanglement modeling known as slip-links. Recently, slip-links were shown to possess important advantages over tube models, namely they have strong connections to atomistic, multichain levels of description, agree with non-equilibrium thermodynamics, are applicable to any chain architecture and can be used in linear or non-linear rheology. We present a hierarchy of slip-link models that are connected to each other through successive coarse graining. Models in the hierarchy are consistent in their overlapping domains of applicability in order to allow a straightforward mapping of parameters. In particular, the most--detailed level of description has four parameters, three of which can be determined directly from atomistic simulations. On the other hand, the least--detailed member of the hierarchy is numerically accessible, and allows for non-equilibrium flow predictions of complex chain architectures. Using GPU implementation these predictions can be obtained in minutes of computational time on a single desktop equipped with a mainstream gaming GPU. The GPU code is available online for free download.

  1. A multi-physics and multi-scale lumped parameter model of cardiac contraction of the left ventricle: a conceptual model from the protein to the organ scale.

    PubMed

    Bhattacharya-Ghosh, Benjamin; Schievano, Silvia; Díaz-Zuccarini, Vanessa

    2012-10-01

    In cardiovascular computational physiology the importance of understanding cardiac contraction as a multi-scale process is of paramount importance to understand causality across different scales. Within this study, a multi-scale and multi-physics model of the left ventricle that connects the process of cardiac excitation and contraction from the protein to the organ level is presented in a novel way. The model presented here includes the functional description of a cardiomyocyte (cellular scale), which explains the dynamic behaviour of the calcium concentration within the cell whilst an action potential develops. The cell domain is coupled to a domain that determines the kinetics of the sliding filament mechanism (protein level), which is at the basis of cardiac contraction. These processes are then linked to the generation of muscular force and from there to the generation of pressure inside the ventricle. This multi-scale model presents a coherent and unified way to describe cardiac contraction from the protein to the organ level.

  2. Capturing recrystallization of metals with a multi-scale materials model

    SciTech Connect

    D. A. Hughes; D. J. Bammann; A. Godfrey; V. C. Prantil; E. A. Holm; M. A. Miodownik; D. C. Chrzan; M. T. Lusk

    2000-04-01

    The final report for a Laboratory Directed Research and Development project entitled, ``Capturing Recrystallization of Metals in a Multiscale Materials Model'' is presented. In this project, deformation and recrystallization processes have been followed experimentally and theoretically in order to incorporate essential mechanisms from the defect (dislocation) and grain size length scales. A nonlinear rotational gradient theory has been developed which enables the incorporation of microstructural parameters. The evolution of these parameters during deformation and recrystallization has been characterized qualitatively and quantitatively, applying various electron optic techniques ranging over several length scales. The theoretical and experimental framework developed is general. It has been exemplified by an application to recrystallization in single crystals and bicrystals of aluminum. The recrystallization process has been modeled using a 3-D model for the changes in key structural parameters during recrystallization.

  3. Multi-scale analysis for microscopic models in materials science and cell biology

    NASA Astrophysics Data System (ADS)

    Kho, Alvin Thong-Juak

    2000-10-01

    In Part I, we study the effects of random fluctuations included in microscopic models for phase transitions, to macroscopic interface flows. We first derive asymptotically a stochastic mean curvature evolution law from the stochastic Ginzburg-Landau model and develop a corresponding level set formulation. Secondly we demonstrate numerically, using stochastic Ginzburg-Landau and Ising algorithms, that microscopic random perturbations resolve geometric and numerical instabilities in the event of non-uniqueness in the corresponding deterministic flow. In Part II, we analyze the effects of random local linker length variability on the global morphology of a very long, linear, homogeneous chromatin fiber that is modelled as a diffusion process which is parametrized by arclength under a suitable spatial re-scaling. We obtain a Fokker-Planck equation for the process whose solution, a probability density function describes the folding.

  4. Stem cell competition in the gut: insights from multi-scale computational modelling.

    PubMed

    Thalheim, Torsten; Buske, Peter; Przybilla, Jens; Rother, Karen; Loeffler, Markus; Galle, Joerg

    2016-08-01

    Three-dimensional (3D) computational tissue models can provide a comprehensive description of tissue dynamics at the molecular, cellular and tissue level. Moreover, they can support the development of hypotheses about cellular interactions and about synergies between major signalling pathways. We exemplify these capabilities by simulation of a 3D single-cell-based model of mouse small intestinal crypts. We analyse the impact of lineage specification, distribution and cellular lifespan on clonal competition and study effects of Notch- and Wnt activation on fixation of mutations within the tissue. Based on these results, we predict that experimentally observed synergistic effects between autonomous Notch- and Wnt signalling in triggering intestinal tumourigenesis originate in the suppression of Wnt-dependent secretory lineage specification by Notch, giving rise to an increased fixation probability of Wnt-activating mutations. Our study demonstrates that 3D computational tissue models can support a mechanistic understanding of long-term tissue dynamics under homeostasis and during transformation. PMID:27534699

  5. Stem cell competition in the gut: insights from multi-scale computational modelling

    PubMed Central

    Buske, Peter; Przybilla, Jens; Rother, Karen; Loeffler, Markus

    2016-01-01

    Three-dimensional (3D) computational tissue models can provide a comprehensive description of tissue dynamics at the molecular, cellular and tissue level. Moreover, they can support the development of hypotheses about cellular interactions and about synergies between major signalling pathways. We exemplify these capabilities by simulation of a 3D single-cell-based model of mouse small intestinal crypts. We analyse the impact of lineage specification, distribution and cellular lifespan on clonal competition and study effects of Notch- and Wnt activation on fixation of mutations within the tissue. Based on these results, we predict that experimentally observed synergistic effects between autonomous Notch- and Wnt signalling in triggering intestinal tumourigenesis originate in the suppression of Wnt-dependent secretory lineage specification by Notch, giving rise to an increased fixation probability of Wnt-activating mutations. Our study demonstrates that 3D computational tissue models can support a mechanistic understanding of long-term tissue dynamics under homeostasis and during transformation. PMID:27534699

  6. Effects of Energy Development on Hydrologic Response: a Multi-Scale Modeling Approach

    NASA Astrophysics Data System (ADS)

    Vithanage, J.; Miller, S. N.; Berendsen, M.; Caffrey, P. A.; Bellis, J.; Schuler, R.

    2013-12-01

    Potential impacts of energy development on surface hydrology in western Wyoming were assessed using spatially explicit hydrological models. Currently there are proposals to develop over 800 new oil and gas wells in the 218,000 acre-sized LaBarge development area that abuts the Wyoming Range and contributes runoff to the Upper Green River (approximately 1 well per 2 square miles). The intensity of development raises questions relating to impacts on the hydrological cycle, water quality, erosion and sedimentation. We developed landscape management scenarios relating to current disturbance and proposed actions put forth by the energy operators to provide inputs to spatially explicit hydrologic models. Differences between the scenarios were derived to quantify the changes and analyse the impacts to the project area. To perform this research, the Automated Watershed Assessment Tool (AGWA) was enhanced by adding different management practices suitable for the region, including the reclamation of disturbed lands over time. The AGWA interface was used to parameterize and execute two hydrologic models: the Soil and Water Assessment Tool (SWAT) and the KINEmatic Runoff and EROSion model (KINEROS2). We used freely available data including SSURGO soils, Multi-Resolution Landscape Consortium (MRLC) land cover, and 10m resolution terrain data to derive suitable initial parameters for the models. The SWAT model was manually calibrated using an innovative method at the monthly level; observed daily rainfall and temperature inputs were used as a function of elevation considering the local climate effects. Higher temporal calibration was not possible due to a lack of adequate climate and runoff data. The Nash Sutcliff efficiencies of two calibrated watersheds at the monthly scale exceeded 0.95. Results of the AGWA/SWAT simulations indicate a range of sensitivity to disturbance due to heterogeneous soil and terrain characteristics over a simulated time period of 10 years. The KINEROS

  7. Multi-Scale Agent-Based Multiple Myeloma Cancer Modeling and the Related Study of the Balance between Osteoclasts and Osteoblasts

    PubMed Central

    Qiao, Minna; Wu, Dan; Carey, Michelle; Zhou, Xiaobo; Zhang, Le

    2015-01-01

    Research Background Currently, multiple myeloma is the second most common hematological malignancy in the U.S., constituting 1% of all cancers. With conventional treatment, the median survival time is typically 3–4 years, although it can be extended to 5–7 years or longer with advanced treatments. Recent research indicated that an increase in osteoclast (OC) activity is often associated withmultiple myeloma (MM) and that a decrease inosteoblast (OB) activity contributesto the osteolytic lesions in MM. Normally, the populations of OCs and OBs are inequilibrium, and an imbalance in this statecontributes to the development of lesions. Research procedures A multi-scale agent-based multiple myeloma model was developed to simulate the proliferation, migration and death of OBs and OCs. Subsequently, this model was employed to investigate the efficacy of thethree most commonly used drugs for MM treatment under the following two premises: the reduction in the progression of MM and the re-establishment of the equilibrium between OCs and OBs. Research purposes The simulated results not only demonstrated the capacity of the model to choose optimal combinations of the drugs but also showed that the optimal use of the three drugs can restore the balance between OCs and OBs as well as kill MMs. Furthermore, the drug synergism analysis function of the model revealed that restoring the balance between OBs and OCs can significantly increase the efficacy of drugs against tumor cells. PMID:26659358

  8. Specimen-specific multi-scale model for the anisotropic elastic constants of human cortical bone.

    PubMed

    Deuerling, Justin M; Yue, Weimin; Espinoza Orías, Alejandro A; Roeder, Ryan K

    2009-09-18

    The anisotropic elastic constants of human cortical bone were predicted using a specimen-specific micromechanical model that accounted for structural parameters across multiple length scales. At the nano-scale, the elastic constants of the mineralized collagen fibril were estimated from measured volume fractions of the constituent phases, namely apatite crystals and Type I collagen. The elastic constants of the extracellular matrix (ECM) were predicted using the measured orientation distribution function (ODF) for the apatite crystals to average the contribution of misoriented mineralized collagen fibrils. Finally, the elastic constants of cortical bone tissue were determined by accounting for the measured volume fraction of Haversian porosity within the ECM. Model predictions using the measured apatite crystal ODF were not statistically different from experimental measurements for both the magnitude and anisotropy of elastic constants. In contrast, model predictions using common idealized assumptions of perfectly aligned or randomly oriented apatite crystals were significantly different from the experimental measurements. A sensitivity analysis indicated that the apatite crystal volume fraction and ODF were the most influential structural parameters affecting model predictions of the magnitude and anisotropy, respectively, of elastic constants.

  9. Multi-scale modeling for the transmission of influenza and the evaluation of interventions toward it

    PubMed Central

    Guo, Dongmin; Li, King C.; Peters, Timothy R.; Snively, Beverly M.; Poehling, Katherine A.; Zhou, Xiaobo

    2015-01-01

    Mathematical modeling of influenza epidemic is important for analyzing the main cause of the epidemic and finding effective interventions towards it. The epidemic is a dynamic process. In this process, daily infections are caused by people's contacts, and the frequency of contacts can be mainly influenced by their cognition to the disease. The cognition is in turn influenced by daily illness attack rate, climate, and other environment factors. Few existing methods considered the dynamic process in their models. Therefore, their prediction results can hardly be explained by the mechanisms of epidemic spreading. In this paper, we developed a heterogeneous graph modeling approach (HGM) to describe the dynamic process of influenza virus transmission by taking advantage of our unique clinical data. We built social network of studied region and embedded an Agent-Based Model (ABM) in the HGM to describe the dynamic change of an epidemic. Our simulations have a good agreement with clinical data. Parameter sensitivity analysis showed that temperature influences the dynamic of epidemic significantly and system behavior analysis showed social network degree is a critical factor determining the size of an epidemic. Finally, multiple scenarios for vaccination and school closure strategies were simulated and their performance was analyzed. PMID:25757402

  10. Multi-scale modeling for the transmission of influenza and the evaluation of interventions toward it.

    PubMed

    Guo, Dongmin; Li, King C; Peters, Timothy R; Snively, Beverly M; Poehling, Katherine A; Zhou, Xiaobo

    2015-01-01

    Mathematical modeling of influenza epidemic is important for analyzing the main cause of the epidemic and finding effective interventions towards it. The epidemic is a dynamic process. In this process, daily infections are caused by people's contacts, and the frequency of contacts can be mainly influenced by their cognition to the disease. The cognition is in turn influenced by daily illness attack rate, climate, and other environment factors. Few existing methods considered the dynamic process in their models. Therefore, their prediction results can hardly be explained by the mechanisms of epidemic spreading. In this paper, we developed a heterogeneous graph modeling approach (HGM) to describe the dynamic process of influenza virus transmission by taking advantage of our unique clinical data. We built social network of studied region and embedded an Agent-Based Model (ABM) in the HGM to describe the dynamic change of an epidemic. Our simulations have a good agreement with clinical data. Parameter sensitivity analysis showed that temperature influences the dynamic of epidemic significantly and system behavior analysis showed social network degree is a critical factor determining the size of an epidemic. Finally, multiple scenarios for vaccination and school closure strategies were simulated and their performance was analyzed. PMID:25757402

  11. Evaluation of Cartosat-1 Multi-Scale Digital Surface Modelling Over France

    PubMed Central

    Gianinetto, Marco

    2009-01-01

    On 5 May 2005, the Indian Space Research Organization launched Cartosat-1, the eleventh satellite of its constellation, dedicated to the stereo viewing of the Earth's surface for terrain modeling and large-scale mapping, from the Satish Dhawan Space Centre (India). In early 2006, the Indian Space Research Organization started the Cartosat-1 Scientific Assessment Programme, jointly established with the International Society for Photogrammetry and Remote Sensing. Within this framework, this study evaluated the capabilities of digital surface modeling from Cartosat-1 stereo data for the French test sites of Mausanne les Alpilles and Salon de Provence. The investigation pointed out that for hilly territories it is possible to produce high-resolution digital surface models with a root mean square error less than 7.1 m and a linear error at 90% confidence level less than 9.5 m. The accuracy of the generated digital surface models also fulfilled the requirements of the French Reference 3D®, so Cartosat-1 data may be used to produce or update such kinds of products. PMID:22412311

  12. Northeast Coastal Ocean Forecast System (NECOFS): A Multi-scale Global-Regional-Estuarine FVCOM Model

    NASA Astrophysics Data System (ADS)

    Beardsley, R. C.; Chen, C.

    2014-12-01

    The Northeast Coastal Ocean Forecast System (NECOFS) is a global-regional-estuarine integrated atmosphere/surface wave/ocean forecast model system designed for the northeast US coastal region covering a computational domain from central New Jersey to the eastern end of the Scotian Shelf. The present system includes 1) the mesoscale meteorological model WRF (Weather Research and Forecasting); 2) the regional-domain FVCOM covering the Gulf of Maine/Georges Bank/New England Shelf region (GOM-FVCOM); 3) the unstructured-grid surface wave model (FVCOM-SWAVE) modified from SWAN with the same domain as GOM-FVCOM; 3) the Mass coastal FVCOM with inclusion of inlets, estuaries and intertidal wetlands; and 4) three subdomain wave-current coupled inundation FVCOM systems in Scituate, MA, Hampton River, NH and Mass Bay, MA. GOM-FVCOM grid features unstructured triangular meshes with horizontal resolution of ~ 0.3-25 km and a hybrid terrain-following vertical coordinate with a total of 45 layers. The Mass coastal FVCOM grid is configured with triangular meshes with horizontal resolution up to ~10 m, and 10 layers in the vertical. Scituate, Hampton River and Mass Bay inundation model grids include both water and land with horizontal resolution up to ~5-10 m and 10 vertical layers. GOM-FVCOM is driven by surface forcing from WRF model output configured for the region (with 9-km resolution), the COARE3 bulk air-sea flux algorithm, local river discharges, and tidal forcing constructed by eight constituents and subtidal forcing on the boundary nested to the Global-FVCOM. SWAVE is driven by the same WRF wind field with wave forcing at the boundary nested to Wave Watch III configured for the northwestern Atlantic region. The Mass coastal FVCOM and three inundation models are connected with GOM-FVCOM through one-way nesting in the common boundary zones. The Mass coastal FVCOM is driven by the same surface forcing as GOM-FVCOM. The nesting boundary conditions for the inundation models

  13. Multi-Scale Computational Model of Three-Dimensional Hemodynamics within a Deformable Full-Body Arterial Network

    PubMed Central

    Xiao, Nan; Humphrey, Jay D.; Figueroa, C. Alberto

    2012-01-01

    In this article, we present a computational multi-scale model of fully three-dimensional and unsteady hemodynamics within the primary large arteries in the human. Computed tomography image data from two different patients were used to reconstruct a nearly complete network of the major arteries from head to foot. A linearized coupled-momentum method for fluid-structure-interaction was used to describe vessel wall deformability and a multi-domain method for outflow boundary condition specification was used to account for the distal circulation. We demonstrated that physiologically realistic results can be obtained from the model by comparing simulated quantities such as regional blood flow, pressure and flow waveforms, and pulse wave velocities to known values in the literature. We also simulated the impact of age-related arterial stiffening on wave propagation phenomena by progressively increasing the stiffness of the central arteries and found that the predicted effects on pressure amplification and pulse wave velocity are in agreement with findings in the clinical literature. This work demonstrates the feasibility of three-dimensional techniques for simulating hemodynamics in a full-body compliant arterial network. PMID:23729840

  14. Multi-scale computational model of three-dimensional hemodynamics within a deformable full-body arterial network

    SciTech Connect

    Xiao, Nan; Humphrey, Jay D.; Figueroa, C. Alberto

    2013-07-01

    In this article, we present a computational multi-scale model of fully three-dimensional and unsteady hemodynamics within the primary large arteries in the human. Computed tomography image data from two different patients were used to reconstruct a nearly complete network of the major arteries from head to foot. A linearized coupled-momentum method for fluid–structure-interaction was used to describe vessel wall deformability and a multi-domain method for outflow boundary condition specification was used to account for the distal circulation. We demonstrated that physiologically realistic results can be obtained from the model by comparing simulated quantities such as regional blood flow, pressure and flow waveforms, and pulse wave velocities to known values in the literature. We also simulated the impact of age-related arterial stiffening on wave propagation phenomena by progressively increasing the stiffness of the central arteries and found that the predicted effects on pressure amplification and pulse wave velocity are in agreement with findings in the clinical literature. This work demonstrates the feasibility of three-dimensional techniques for simulating hemodynamics in a full-body compliant arterial network.

  15. On multi-scale percolation behaviour of the effective conductivity for the lattice model with interacting particles

    NASA Astrophysics Data System (ADS)

    Wiśniowski, R.; Olchawa, W.; Frączek, D.; Piasecki, R.

    2016-02-01

    Recently, the effective medium approach (EMA) using 2×2 basic cluster of model lattice sites to predict the conductivity of interacting microemulsion droplets has been presented by Hattori et al. To make a step aside from pure applications, we studied earlier a multi-scale percolation, employing any k× k basic cluster for non-interacting particles. Here, with interactions included, we examine in what way they alter the percolation threshold for any cluster case. We found that at a fixed length scale k, the interaction reduces the range of shifts of the percolation threshold. To determine the critical concentrations, the simplified EMA-model is used. It diminishes the number of local conductivities into two main ones. In the presence of a dominance of the repulsive interaction over the thermal energy, the exact percolation thresholds at two small scales can be revealed from analytical formulas. Furthermore, at large scales, the highest possible value of the estimated threshold can be obtained.

  16. 3D Visualization of Hydrological Model Outputs For a Better Understanding of Multi-Scale Phenomena

    NASA Astrophysics Data System (ADS)

    Richard, J.; Schertzer, D. J. M.; Tchiguirinskaia, I.

    2014-12-01

    During the last decades, many hydrological models has been created to simulate extreme events or scenarios on catchments. The classical outputs of these models are 2D maps, time series or graphs, which are easily understood by scientists, but not so much by many stakeholders, e.g. mayors or local authorities, and the general public. One goal of the Blue Green Dream project is to create outputs that are adequate for them. To reach this goal, we decided to convert most of the model outputs into a unique 3D visualization interface that combines all of them. This conversion has to be performed with an hydrological thinking to keep the information consistent with the context and the raw outputs.We focus our work on the conversion of the outputs of the Multi-Hydro (MH) model, which is physically based, fully distributed and with a GIS data interface. MH splits the urban water cycle into 4 components: the rainfall, the surface runoff, the infiltration and the drainage. To each of them, corresponds a modeling module with specific inputs and outputs. The superimposition of all this information will highlight the model outputs and help to verify the quality of the raw input data. For example, the spatial and the time variability of the rain generated by the rainfall module will be directly visible in 4D (3D + time) before running a full simulation. It is the same with the runoff module: because the result quality depends of the resolution of the rasterized land use, it will confirm or not the choice of the cell size.As most of the inputs and outputs are GIS files, two main conversions will be applied to display the results into 3D. First, a conversion from vector files to 3D objects. For example, buildings are defined in 2D inside a GIS vector file. Each polygon can be extruded with an height to create volumes. The principle is the same for the roads but an intrusion, instead of an extrusion, is done inside the topography file. The second main conversion is the raster

  17. A multi-scale comparison of modeled and observed seasonal methane emissions in northern wetlands

    NASA Astrophysics Data System (ADS)

    Xu, Xiyan; Riley, William J.; Koven, Charles D.; Billesbach, Dave P.; Chang, Rachel Y.-W.; Commane, Róisín; Euskirchen, Eugénie S.; Hartery, Sean; Harazono, Yoshinobu; Iwata, Hiroki; McDonald, Kyle C.; Miller, Charles E.; Oechel, Walter C.; Poulter, Benjamin; Raz-Yaseef, Naama; Sweeney, Colm; Torn, Margaret; Wofsy, Steven C.; Zhang, Zhen; Zona, Donatella

    2016-09-01

    Wetlands are the largest global natural methane (CH4) source, and emissions between 50 and 70° N latitude contribute 10-30 % to this source. Predictive capability of land models for northern wetland CH4 emissions is still low due to limited site measurements, strong spatial and temporal variability in emissions, and complex hydrological and biogeochemical dynamics. To explore this issue, we compare wetland CH4 emission predictions from the Community Land Model 4.5 (CLM4.5-BGC) with site- to regional-scale observations. A comparison of the CH4 fluxes with eddy flux data highlighted needed changes to the model's estimate of aerenchyma area, which we implemented and tested. The model modification substantially reduced biases in CH4 emissions when compared with CarbonTracker CH4 predictions. CLM4.5 CH4 emission predictions agree well with growing season (May-September) CarbonTracker Alaskan regional-level CH4 predictions and site-level observations. However, CLM4.5 underestimated CH4 emissions in the cold season (October-April). The monthly atmospheric CH4 mole fraction enhancements due to wetland emissions are also assessed using the Weather Research and Forecasting-Stochastic Time-Inverted Lagrangian Transport (WRF-STILT) model coupled with daily emissions from CLM4.5 and compared with aircraft CH4 mole fraction measurements from the Carbon in Arctic Reservoirs Vulnerability Experiment (CARVE) campaign. Both the tower and aircraft analyses confirm the underestimate of cold-season CH4 emissions by CLM4.5. The greatest uncertainties in predicting the seasonal CH4 cycle are from the wetland extent, cold-season CH4 production and CH4 transport processes. We recommend more cold-season experimental studies in high-latitude systems, which could improve the understanding and parameterization of ecosystem structure and function during this period. Predicted CH4 emissions remain uncertain, but we show here that benchmarking against observations across spatial scales can

  18. Hierarchical analysis and multi-scale modelling of rat cortical and trabecular bone

    PubMed Central

    Oftadeh, Ramin; Entezari, Vahid; Spörri, Guy; Villa-Camacho, Juan C.; Krigbaum, Henry; Strawich, Elsa; Graham, Lila; Rey, Christian; Chiu, Hank; Müller, Ralph; Hashemi, Hamid Nayeb; Vaziri, Ashkan; Nazarian, Ara

    2015-01-01

    The aim of this study was to explore the hierarchical arrangement of structural properties in cortical and trabecular bone and to determine a mathematical model that accurately predicts the tissue's mechanical properties as a function of these indices. By using a variety of analytical techniques, we were able to characterize the structural and compositional properties of cortical and trabecular bones, as well as to determine the suitable mathematical model to predict the tissue's mechanical properties using a continuum micromechanics approach. Our hierarchical analysis demonstrated that the differences between cortical and trabecular bone reside mainly at the micro- and ultrastructural levels. By gaining a better appreciation of the similarities and differences between the two bone types, we would be able to provide a better assessment and understanding of their individual roles, as well as their contribution to bone health overall. PMID:25808343

  19. Multi-scale climate change modeling study over the Greater Horn of Africa

    NASA Astrophysics Data System (ADS)

    Bowden, Jared Heath

    There has been limited regional climate modeling (RCM) studies of climate change over the Greater Horn of Africa because of challenges in evaluating model performance with a limited observational network. The ultimate goal of this study was to provide a RCM climate change projection for the GHA. RCM climate change projections are particularly important for the GHA because the surface boundary forcing varies on horizontal scales not resolved by the IPCC General Circulation Models (GCMs) used for current regional climate change assessment. This study adopted several steps to provide optimal RCM projections and understand the uncertainty and added value of the RCM projections. These steps include the following: (1) model customization; (2) multi-year continuous RCM simulation with Reanalysis ICBCs and a single GCM; (3) GCM mean error; (4) A2 GCM projections; (5) A2 RCM projections; (6) modified ICBC approach. The RCM was customized with particular interest in precipitation processes. The customization found that the convective scheme of MIT-Emanuel in conjunction with reducing the relative humidity for threshold for cloud formation provided the most realistic simulation in terms of spatial distribution, convective partition, rainfall totals and temperature bias when compared with observations. The above RCM customization run for multiple years illustrated the RCM has more value for temperature than precipitation. The RCM was able to capture the inter-annual temperature variability, but the positive precipitation bias limited the models ability for inter-annual precipitation variability. However, the RCM was able to capture lower frequency modes of variability for precipitation. Comparison of multi-year RCM simulations using the GCM and Reanalysis lateral boundary forcing implied that the lateral boundary forcing is more important to the RCM solution than errors internal to the RCM. Comparison of the GCMs mean errors illustrated that the mean average performance

  20. A multi-scale conceptual model of fire and disease interactions in North American forests

    NASA Astrophysics Data System (ADS)

    Varner, J. M.; Kreye, J. K.; Sherriff, R.; Metz, M.

    2013-12-01

    One aspect of global change with increasing attention is the interactions between irruptive pests and diseases and wildland fire behavior and effects. These pests and diseases affect fire behavior and effects in spatially and temporally complex ways. Models of fire and pathogen interactions have been constructed for individual pests or diseases, but to date, no synthesis of this complexity has been attempted. Here we synthesize North American fire-pathogen interactions into syndromes with similarities in spatial extent and temporal duration. We base our models on fire interactions with three examples: sudden oak death (caused by the pathogen Phytopthora ramorum) and the native tree tanoak (Notholithocarpus densiflorus); mountain pine beetle (Dendroctonus ponderosae) and western Pinus spp.; and hemlock woolly adelgid (Adelges tsugae) on Tsuga spp. We evaluate each across spatial (severity of attack from branch to landscape scale) and temporal scales (from attack to decades after) and link each change to its coincident effects on fuels and potential fire behavior. These syndromes differ in their spatial and temporal severity, differentially affecting windows of increased or decreased community flammability. We evaluate these models with two examples: the recently emergent ambrosia beetle-vectored laurel wilt (caused by the pathogen Raffaelea lauricola) in native members of the Lauraceae and the early 20th century chestnut blight (caused by the pathogen Cryphonectria parasitica) that led to the decline of American chestnut (Castanea dentata). Some changes (e.g., reduced foliar moisture content) have short-term consequences for potential fire behavior while others (functional extirpation) have more complex indirect effects on community flammability. As non-native emergent diseases and pests continue, synthetic models that aid in prediction of fire behavior and effects will enable the research and management community to prioritize mitigation efforts to realized effects.

  1. Surface Roughness Retrieval By Inversion Of Hapke Model: A Multi-scale Approach

    NASA Astrophysics Data System (ADS)

    Labarre, S.; Ferrari, C. C.; Jacquemoud, S.

    2015-12-01

    Surface roughness is a key property of soils that affects the various processes involved in their evolution such as solar absorption, erosion or moisture, both on Earth and other Solar System surfaces. In the 80's, B.Hapke provided an approximate analytic solution for the bidirectional reflectance distribution function (BRDF) of a particulate medium and, later on, included the effect of surface roughness as a correction factor for the BRDF of a smooth surface. The effect of roughness on the BRDF is modeled as a shadowing function of the so-called roughness parameter, which is the mean slope angle of the facets composing the surface integrated over all scales from the sub-millimeter to the kilometer scales. Hapke model is widely used in planetary sciences to retrieve the roughness parameter from observed BRDFs. Yet the physical meaning of the retrieved roughness is not clear as the scale at which it happens is not defined. This work aims at understanding the relative impact of the roughness defined at each scale to the BRDF in order to test the ability of the singly retrieved roughness parameter at describing the ground truth. We propose to perform a wavelet analysis on meter-sized digital elevation models (DEM) generated from various volcanic and sedimentary terrains at high-mm-scale spatial resolution. It consists in splitting the DEM in several spatial frequencies and in simulating the BRDF at each scale with a ray-tracing code. Also the global BRDF is simulated so that the relative contribution of each scale can be studied. Then the Hapke model is fitted to the global BRDF to retrieve the roughness parameter. We will expose and discuss the results of this study. Figure: BRDF of a'a lava DEM simulated at varying azimut (φi) and incidence angles (i), in the principal plan. The direction of the light source is given by the colored squares. Mean slope angle of the surface is 36°.

  2. A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation

    PubMed Central

    Hester, Susan D.; Belmonte, Julio M.; Gens, J. Scott; Clendenon, Sherry G.; Glazier, James A.

    2011-01-01

    Somitogenesis, the formation of the body's primary segmental structure common to all vertebrate development, requires coordination between biological mechanisms at several scales. Explaining how these mechanisms interact across scales and how events are coordinated in space and time is necessary for a complete understanding of somitogenesis and its evolutionary flexibility. So far, mechanisms of somitogenesis have been studied independently. To test the consistency, integrability and combined explanatory power of current prevailing hypotheses, we built an integrated clock-and-wavefront model including submodels of the intracellular segmentation clock, intercellular segmentation-clock coupling via Delta/Notch signaling, an FGF8 determination front, delayed differentiation, clock-wavefront readout, and differential-cell-cell-adhesion-driven cell sorting. We identify inconsistencies between existing submodels and gaps in the current understanding of somitogenesis mechanisms, and propose novel submodels and extensions of existing submodels where necessary. For reasonable initial conditions, 2D simulations of our model robustly generate spatially and temporally regular somites, realistic dynamic morphologies and spontaneous emergence of anterior-traveling stripes of Lfng. We show that these traveling stripes are pseudo-waves rather than true propagating waves. Our model is flexible enough to generate interspecies-like variation in somite size in response to changes in the PSM growth rate and segmentation-clock period, and in the number and width of Lfng stripes in response to changes in the PSM growth rate, segmentation-clock period and PSM length. PMID:21998560

  3. Stress distribution retrieval in granular materials: A multi-scale model and digital image correlation measurements

    NASA Astrophysics Data System (ADS)

    Bruno, Luigi; Decuzzi, Paolo; Gentile, Francesco

    2016-01-01

    The promise of nanotechnology lies in the possibility of engineering matter on the nanoscale and creating technological interfaces that, because of their small scales, may directly interact with biological objects, creating new strategies for the treatment of pathologies that are otherwise beyond the reach of conventional medicine. Nanotechnology is inherently a multiscale, multiphenomena challenge. Fundamental understanding and highly accurate predictive methods are critical to successful manufacturing of nanostructured materials, bio/mechanical devices and systems. In biomedical engineering, and in the mechanical analysis of biological tissues, classical continuum approaches are routinely utilized, even if these disregard the discrete nature of tissues, that are an interpenetrating network of a matrix (the extra cellular matrix, ECM) and a generally large but finite number of cells with a size falling in the micrometer range. Here, we introduce a nano-mechanical theory that accounts for the-non continuum nature of bio systems and other discrete systems. This discrete field theory, doublet mechanics (DM), is a technique to model the mechanical behavior of materials over multiple scales, ranging from some millimeters down to few nanometers. In the paper, we use this theory to predict the response of a granular material to an external applied load. Such a representation is extremely attractive in modeling biological tissues which may be considered as a spatial set of a large number of particulate (cells) dispersed in an extracellular matrix. Possibly more important of this, using digital image correlation (DIC) optical methods, we provide an experimental verification of the model.

  4. Multi-scale occupancy estimation and modelling using multiple detection methods

    USGS Publications Warehouse

    Nichols, James D.; Bailey, Larissa L.; O'Connell, Allan F.; Talancy, Neil W.; Grant, Evan H. Campbell; Gilbert, Andrew T.; Annand, Elizabeth M.; Husband, Thomas P.; Hines, James E.

    2008-01-01

    Occupancy estimation and modelling based on detection–nondetection data provide an effective way of exploring change in a species’ distribution across time and space in cases where the species is not always detected with certainty. Today, many monitoring programmes target multiple species, or life stages within a species, requiring the use of multiple detection methods. When multiple methods or devices are used at the same sample sites, animals can be detected by more than one method.We develop occupancy models for multiple detection methods that permit simultaneous use of data from all methods for inference about method-specific detection probabilities. Moreover, the approach permits estimation of occupancy at two spatial scales: the larger scale corresponds to species’ use of a sample unit, whereas the smaller scale corresponds to presence of the species at the local sample station or site.We apply the models to data collected on two different vertebrate species: striped skunks Mephitis mephitis and red salamanders Pseudotriton ruber. For striped skunks, large-scale occupancy estimates were consistent between two sampling seasons. Small-scale occupancy probabilities were slightly lower in the late winter/spring when skunks tend to conserve energy, and movements are limited to males in search of females for breeding. There was strong evidence of method-specific detection probabilities for skunks. As anticipated, large- and small-scale occupancy areas completely overlapped for red salamanders. The analyses provided weak evidence of method-specific detection probabilities for this species.Synthesis and applications. Increasingly, many studies are utilizing multiple detection methods at sampling locations. The modelling approach presented here makes efficient use of detections from multiple methods to estimate occupancy probabilities at two spatial scales and to compare detection probabilities associated with different detection methods. The models can be

  5. Multi-scale occupancy estimation and modelling using multiple detection methods

    USGS Publications Warehouse

    Nichols, J.D.; Bailey, L.L.; O'Connell, A.F.; Talancy, N.W.; Grant, E.H.C.; Gilbert, A.T.; Annand, E.M.; Husband, T.P.; Hines, J.E.

    2008-01-01

    1. Occupancy estimation and modelling based on detection?nondetection data provide an effective way of exploring change in a species' distribution across time and space in cases where the species is not always detected with certainty. Today, many monitoring programmes target multiple species, or life stages within a species, requiring the use of multiple detection methods. When multiple methods or devices are used at the same sample sites, animals can be detected by more than one method. 2. We develop occupancy models for multiple detection methods that permit simultaneous use of data from all methods for inference about method-specific detection probabilities. Moreover, the approach permits estimation of occupancy at two spatial scales: the larger scale corresponds to species' use of a sample unit, whereas the smaller scale corresponds to presence of the species at the local sample station or site. 3. We apply the models to data collected on two different vertebrate species: striped skunks Mephitis mephitis and red salamanders Pseudotriton ruber. For striped skunks, large-scale occupancy estimates were consistent between two sampling seasons. Small-scale occupancy probabilities were slightly lower in the late winter/spring when skunks tend to conserve energy, and movements are limited to males in search of females for breeding. There was strong evidence of method-specific detection probabilities for skunks. As anticipated, large- and small-scale occupancy areas completely overlapped for red salamanders. The analyses provided weak evidence of method-specific detection probabilities for this species. 4. Synthesis and applications. Increasingly, many studies are utilizing multiple detection methods at sampling locations. The modelling approach presented here makes efficient use of detections from multiple methods to estimate occupancy probabilities at two spatial scales and to compare detection probabilities associated with different detection methods. The models can

  6. Multi-scale occupancy estimation and modelling using multiple detection methods

    USGS Publications Warehouse

    Nichols, J.D.; Bailey, L.L.; O'Connell, Jr.; Talancy, N.W.; Campbell, Grant E.H.; Gilbert, A.T.; Annand, E.M.; Husband, T.P.; Hines, J.E.

    2008-01-01

    1. Occupancy estimation and modelling based on detection-nondetection data provide an effective way of exploring change in a species' distribution across time and space in cases where the species is not always detected with certainty. Today, many monitoring programmes target multiple species, or life stages within a species, requiring the use of multiple detection methods. When multiple methods or devices are used at the same sample sites, animals can be detected by more than one method. 2. We develop occupancy models for multiple detection methods that permit simultaneous use of data from all methods for inference about method-specific detection probabilities. Moreover, the approach permits estimation of occupancy at two spatial scales: the larger scale corresponds to species' use of a sample unit, whereas the smaller scale corresponds to presence of the species at the local sample station or site. 3. We apply the models to data collected on two different vertebrate species: striped skunks Mephitis mephitis and red salamanders Pseudotriton ruber. For striped skunks, large-scale occupancy estimates were consistent between two sampling seasons. Small-scale occupancy probabilities were slightly lower in the late winter/spring when skunks tend to conserve energy, and movements are limited to males in search of females for breeding. There was strong evidence of method-specific detection probabilities for skunks. As anticipated, large- and small-scale occupancy areas completely overlapped for red salamanders. The analyses provided weak evidence of method-specific detection probabilities for this species. 4. Synthesis and applications. Increasingly, many studies are utilizing multiple detection methods at sampling locations. The modelling approach presented here makes efficient use of detections from multiple methods to estimate occupancy probabilities at two spatial scales and to compare detection probabilities associated with different detection methods. The models can

  7. Response normalization and blur adaptation: Data and multi-scale model

    PubMed Central

    Elliott, Sarah L.; Georgeson, Mark A.; Webster, Michael A.

    2011-01-01

    Adapting to blurred or sharpened images alters perceived blur of a focused image (M. A. Webster, M. A. Georgeson, & S. M. Webster, 2002). We asked whether blur adaptation results in (a) renormalization of perceived focus or (b) a repulsion aftereffect. Images were checkerboards or 2-D Gaussian noise, whose amplitude spectra had (log–log) slopes from −2 (strongly blurred) to 0 (strongly sharpened). Observers adjusted the spectral slope of a comparison image to match different test slopes after adaptation to blurred or sharpened images. Results did not show repulsion effects but were consistent with some renormalization. Test blur levels at and near a blurred or sharpened adaptation level were matched by more focused slopes (closer to 1/f) but with little or no change in appearance after adaptation to focused (1/f) images. A model of contrast adaptation and blur coding by multiple-scale spatial filters predicts these blur aftereffects and those of Webster et al. (2002). A key proposal is that observers are pre-adapted to natural spectra, and blurred or sharpened spectra induce changes in the state of adaptation. The model illustrates how norms might be encoded and recalibrated in the visual system even when they are represented only implicitly by the distribution of responses across multiple channels. PMID:21307174

  8. An integrative, multi-scale, genome-wide model reveals the phenotypic landscape of Escherichia coli

    PubMed Central

    Carrera, Javier; Estrela, Raissa; Luo, Jing; Rai, Navneet; Tsoukalas, Athanasios; Tagkopoulos, Ilias

    2014-01-01

    Given the vast behavioral repertoire and biological complexity of even the simplest organisms, accurately predicting phenotypes in novel environments and unveiling their biological organization is a challenging endeavor. Here, we present an integrative modeling methodology that unifies under a common framework the various biological processes and their interactions across multiple layers. We trained this methodology on an extensive normalized compendium for the gram-negative bacterium Escherichia coli, which incorporates gene expression data for genetic and environmental perturbations, transcriptional regulation, signal transduction, and metabolic pathways, as well as growth measurements. Comparison with measured growth and high-throughput data demonstrates the enhanced ability of the integrative model to predict phenotypic outcomes in various environmental and genetic conditions, even in cases where their underlying functions are under-represented in the training set. This work paves the way toward integrative techniques that extract knowledge from a variety of biological data to achieve more than the sum of their parts in the context of prediction, analysis, and redesign of biological systems. PMID:24987114

  9. Multi-scale coupling strategy for fully two-dimensional and depth-averaged models for granular flows

    NASA Astrophysics Data System (ADS)

    Pudasaini, Shiva P.; Domnik, Birte; Miller, Stephen A.

    2013-04-01

    We developed a full two-dimensional Coulomb-viscoplastic model and applied it for inclined channel flows of granular materials from initiation to their deposition. The model includes the basic features and observed phenomena in dense granular flows like the exhibition of a yield strength and a non-zero slip velocity. A pressure-dependent yield strength is proposed to account for the frictional nature of granular materials. The yield strength can be related to the internal friction angle of the material and plays an important role, for example, in deposition processes. The interaction of the flow with the solid boundary is modelled by a pressure and rate-dependent Coulomb-viscoplastic sliding law. We developed an innovative multi-scale strategy to couple the full two-dimensional, non depth-averaged model (N-DAM) with a one-dimensional, depth-averaged model (DAM). The coupled model reduces computational complexity dramatically by using DAM only in regions with smooth changes of flow variables. The numerics uses N-DAM in regions where depth-averaging becomes inaccurate, for instance, in the initiation and deposition regions, and (particularly) when the flow hits an obstacle or a defense structure. In these regions, momentum transfer must be, and is, considered in all directions. We observe very high coupling performance, and show that the numerical results deviate only slightly from results of the much more cumbersome full two-dimensional model. This shows that the coupled model, which retains all the basic physics of the flow, is an attractive alternative to an expensive, full two-dimensional simulations. We compare simulation results with different experimental data for shock waves appearing in rapid granular flows down inclined channels and impacting a wall. The model predicts the evolution of the strong shock wave and the impact force on a rigid wall for different inclination angles and sliding surfaces. It is demonstrated that the internal friction angle plays an

  10. A multi-scale hybrid long-term morphodynamic model for wave-dominated coasts

    NASA Astrophysics Data System (ADS)

    Zhang, Wenyan; Schneider, Ralf; Harff, Jan

    2012-05-01

    Process-based modules based on conservative equations to solve the transport of waves, currents and sub-aqueous sediment, and behavior-oriented modules based on empirical descriptions of cliff erosion, bed-load and terrestrial aeolian sand transport are coupled with up-scaling measures and stability-maintaining approaches in a parallel code to simulate decadal-to millennial-scale morphological evolution of wave-dominated coasts. An application to the southern Baltic Sea for a hindcast of Holocene morphogenesis of the Darss-Zingst peninsula demonstrates the robustness of the model. The model is then used to investigate the morphogenesis and evolution of spits in an idealized fetch-limited sandy coastal environment. Evolution of the spit system can be categorized into three periods according to the simulation results. In the early period all initial coastline perturbations are amplified due to the high-angle wave effects. Size competition between adjacent spits starts afterwards. Interaction between adjacent spits dominates the middle period. Smaller spits tend to retrogress due to unbalanced sediment budget and this sediment loss feeds further growth of their larger neighbors. The retrograded spits are either smoothed or evolve into barrier-lagoons, and relatively stable large-scale spits originating from larger spits are developed in the late period. Low-frequency storms impinging from a regular high angle onto the coastline facilitate the development of spits in the early period, but become a hindering factor afterwards. Terrestrial aeolian transport not only plays a key role in stabilizing the spits, but is also revealed as an important factor for long-term coastline erosion.

  11. New insights into chromatin folding and dynamics from multi-scale modeling

    NASA Astrophysics Data System (ADS)

    Olson, Wilma

    The dynamic organization of chromatin plays an essential role in the regulation of gene expression and in other fundamental cellular processes. The underlying physical basis of these activities lies in the sequential positioning, chemical composition, and intermolecular interactions of the nucleosomes-the familiar assemblies of roughly 150 DNA base pairs and eight histone proteins-found on chromatin fibers. We have developed a mesoscale model of short nucleosomal arrays and a computational framework that make it possible to incorporate detailed structural features of DNA and histones in simulations of short chromatin constructs with 3-25 evenly spaced nucleosomes. The correspondence between the predicted and observed effects of nucleosome composition, spacing, and numbers on long-range communication between regulatory proteins bound to the ends of designed nucleosome arrays lends credence to the model and to the molecular insights gleaned from the simulated structures. We have extracted effective nucleosome-nucleosome potentials from the mesoscale simulations and introduced the potentials in a larger scale computational treatment of regularly repeating chromatin fibers. Our results reveal a remarkable influence of nucleosome spacing on chromatin flexibility. Small changes in the length of the DNA fragments linking successive nucleosomes introduce marked changes in the local interactions of the nucleosomes and in the spatial configurations of the fiber as a whole. The changes in nucleosome positioning influence the statistical properties of longer chromatin constructs with 100-10,000 nucleosomes. We are investigating the extent to which the `local' interactions of regularly spaced nucleosomes contribute to the corresponding interactions in chains with mixed spacings as a step toward the treatment of fibers with nucleosomes positioned at the sites mapped at base-pair resolution on genomic sequences. Support of the work by USPHS R01 GM 34809 is gratefully acknowledged.

  12. Segmentation of pelvic structures for planning CT using a geometrical shape model tuned by a multi-scale edge detector

    NASA Astrophysics Data System (ADS)

    Martínez, Fabio; Romero, Eduardo; Dréan, Gaël; Simon, Antoine; Haigron, Pascal; de Crevoisier, Renaud; Acosta, Oscar

    2014-03-01

    Accurate segmentation of the prostate and organs at risk in computed tomography (CT) images is a crucial step for radiotherapy planning. Manual segmentation, as performed nowadays, is a time consuming process and prone to errors due to the a high intra- and inter-expert variability. This paper introduces a new automatic method for prostate, rectum and bladder segmentation in planning CT using a geometrical shape model under a Bayesian framework. A set of prior organ shapes are first built by applying principal component analysis to a population of manually delineated CT images. Then, for a given individual, the most similar shape is obtained by mapping a set of multi-scale edge observations to the space of organs with a customized likelihood function. Finally, the selected shape is locally deformed to adjust the edges of each organ. Experiments were performed with real data from a population of 116 patients treated for prostate cancer. The data set was split in training and test groups, with 30 and 86 patients, respectively. Results show that the method produces competitive segmentations w.r.t standard methods (averaged dice = 0.91 for prostate, 0.94 for bladder, 0.89 for rectum) and outperforms the majority-vote multi-atlas approaches (using rigid registration, free-form deformation and the demons algorithm).

  13. Investigation of urban faults in Shenzhen using wavelet multi-scale analysis and modeling of gravity observations

    NASA Astrophysics Data System (ADS)

    Xu, Chuang; Chen, Liang; Liu, Xi-kai

    2016-04-01

    Urban faults in Shenzhen are potential threat to the city security and sustainable development. To improve the knowledge of the Shenzhen fault zone, interpretation and inversion of gravity data were carried out. Bouguer gravity covering the whole Shenzhen city was calculated with a resolution of 1kmx1km. Wavelet multi-scale analysis (MSA) was applied to the Bouguer gravity data to obtain the multilayer residual anomalies corresponding to different depths. In addition, 2D gravity models were constructed along three profiles. The Bouguer gravity anomaly shows a NE-striking high-low-high pattern from northwest to southeast, strongly related to the main faults. According to the result of MSA, the correlation between gravity anomaly and faults is particularly significant from 4 to 12 km depth. The residual gravity with small amplitude in each layer indicates weak tectonic activity in the crust. In the upper layers, positive anomalies along most of faults reveal the upwelling of high-density materials during the past tectonic movements. The multilayer residual anomalies also implicate important information about the faults, such as the vertical extension and the dip direction. The maximum depth of the faults is about 20km. In general, NE-striking faults extend deeper than NW-striking Faults and have a larger dip angle. This study is supported by the National Natural Science Foundation of China (Grant No.41504015) and China Postdoctoral Science Foundation (Grant No.2015M572146).

  14. Segmentation of pelvic structures for planning CT using a geometrical shape model tuned by a multi-scale edge detector.

    PubMed

    Martínez, Fabio; Romero, Eduardo; Dréan, Gaël; Simon, Antoine; Haigron, Pascal; de Crevoisier, Renaud; Acosta, Oscar

    2014-03-21

    Accurate segmentation of the prostate and organs at risk in computed tomography (CT) images is a crucial step for radiotherapy planning. Manual segmentation, as performed nowadays, is a time consuming process and prone to errors due to the a high intra- and inter-expert variability. This paper introduces a new automatic method for prostate, rectum and bladder segmentation in planning CT using a geometrical shape model under a Bayesian framework. A set of prior organ shapes are first built by applying principal component analysis to a population of manually delineated CT images. Then, for a given individual, the most similar shape is obtained by mapping a set of multi-scale edge observations to the space of organs with a customized likelihood function. Finally, the selected shape is locally deformed to adjust the edges of each organ. Experiments were performed with real data from a population of 116 patients treated for prostate cancer. The data set was split in training and test groups, with 30 and 86 patients, respectively. Results show that the method produces competitive segmentations w.r.t standard methods (averaged dice = 0.91 for prostate, 0.94 for bladder, 0.89 for rectum) and outperforms the majority-vote multi-atlas approaches (using rigid registration, free-form deformation and the demons algorithm).

  15. Impact of spatial data resolution on simulated catchment water balances and model performance of the multi-scale TOPLATS model

    NASA Astrophysics Data System (ADS)

    Bormann, H.

    2006-03-01

    This paper analyses the effect of spatial input data resolution on the simulated water balances and flow components using the multi-scale hydrological model TOPLATS. A data set of 25m resolution of the central German Dill catchment (693 km2) is used for investigation. After an aggregation of digital elevation model, soil map and land use classification to 50 m, 75 m, 100 m, 150 m, 200 m, 300 m, 500 m, 1000 m and 2000 m, water balances and water flow components are calculated for the entire Dill catchment as well as for 3 subcatchments without any recalibration. The study shows that model performance measures and simulated water balances almost remain constant for most of the aggregation steps for all investigated catchments. Slight differences in the simulated water balances and statistical quality measures occur for single catchments at the resolution of 50 m to 500 m (e.g. 0-3% for annual stream flow), significant differences at the resolution of 1000 m and 2000 m (e.g. 2-12% for annual stream flow). These differences can be explained by the fact that the statistics of certain input data (land use data in particular as well as soil physical characteristics) changes significantly at these spatial resolutions. The impact of smoothing the relief by aggregation occurs continuously but is barely reflected by the simulation results. To study the effect of aggregation of land use data in detail, in addition to current land use the effect of aggregation on the water balance calculations based on three different land use scenarios is investigated. Land use scenarios were available aiming on economic optimisation of agricultural and forestry practices at different field sizes (0.5 ha, 1.5 ha and 5.0 ha). The changes in water balance terms, induced by aggregation of the land use scenarios, are comparable with respect to catchment water balances compared to the current land use. A correlation analysis between statistics of input data and simulated annual water fluxes only in

  16. Analysis of fracture aperture and roughness using multi-scale computed tomography and numerical modeling

    NASA Astrophysics Data System (ADS)

    Ketcham, R. A.; Thompson, C.; Slottke, D. T.; Cardenas, M. B.; Sharp, J. M.

    2009-05-01

    Open and connected fractures, when present, dominate both fluid flow and solute transport in rock bodies. The transport properties of fracture networks are controlled by the aperture and roughness of the individual fractures. Precise measurement and meaningful characterization of these features is typically problematic, particularly in tandem. Furthermore, the empirical equations used to characterize the effect of surface roughness on fluid flow are derived from artificial configurations, and may not be suitable for natural systems. We have undertaken a multi-tiered study utilizing X-ray computed tomography combined with laboratory experiments and numerical modeling to characterize natural fractures and their flow properties from the dm to the µm scale. We have created and continue to enhance a series of calibrations and procedures to evaluate and maximize our ability to determine, in three dimensions, surface location and aperture in randomly- orientated fractures in heterogeneous natural materials such as granites. Our methods are geared to explicitly take account of the innate blurring of CT data through measurement and deconvolution of a point-spread function. These methods developed for fracture characterization apply to any measurement problem in which the feature being analyzed is small relative to the resolution of the scan data. Our experimental program encompasses both exposed fracture surfaces (skins) and paired surfaces within solid samples which are then subjected to flow testing. High-energy (420-450 kV) X-rays are required to image the larger specimens (>10 cm diameter) that are necessary to maintain a measurable hydraulic head gradient during flow testing. Nominal resolution is approximately 250 µm, but accuracy in locating air-rock interfaces is in the 25-50 µm range. Extracted ~2 cm sections of fracture skins were studied with 225 kV microfocal CT, with nominal resolution of 25 µm and surface-location accuracy of 5-10 µm. Finally, ~5 mm

  17. Probabilistic Downscaling of Remote Sensing Data with Applications for Multi-Scale Biogeochemical Flux Modeling.

    PubMed

    Stoy, Paul C; Quaife, Tristan

    2015-01-01

    Upscaling ecological information to larger scales in space and downscaling remote sensing observations or model simulations to finer scales remain grand challenges in Earth system science. Downscaling often involves inferring subgrid information from coarse-scale data, and such ill-posed problems are classically addressed using regularization. Here, we apply two-dimensional Tikhonov Regularization (2DTR) to simulate subgrid surface patterns for ecological applications. Specifically, we test the ability of 2DTR to simulate the spatial statistics of high-resolution (4 m) remote sensing observations of the normalized difference vegetation index (NDVI) in a tundra landscape. We find that the 2DTR approach as applied here can capture the major mode of spatial variability of the high-resolution information, but not multiple modes of spatial variability, and that the Lagrange multiplier (γ) used to impose the condition of smoothness across space is related to the range of the experimental semivariogram. We used observed and 2DTR-simulated maps of NDVI to estimate landscape-level leaf area index (LAI) and gross primary productivity (GPP). NDVI maps simulated using a γ value that approximates the range of observed NDVI result in a landscape-level GPP estimate that differs by ca 2% from those created using observed NDVI. Following findings that GPP per unit LAI is lower near vegetation patch edges, we simulated vegetation patch edges using multiple approaches and found that simulated GPP declined by up to 12% as a result. 2DTR can generate random landscapes rapidly and can be applied to disaggregate ecological information and compare of spatial observations against simulated landscapes. PMID:26067835

  18. Probabilistic Downscaling of Remote Sensing Data with Applications for Multi-Scale Biogeochemical Flux Modeling

    PubMed Central

    Stoy, Paul C.; Quaife, Tristan

    2015-01-01

    Upscaling ecological information to larger scales in space and downscaling remote sensing observations or model simulations to finer scales remain grand challenges in Earth system science. Downscaling often involves inferring subgrid information from coarse-scale data, and such ill-posed problems are classically addressed using regularization. Here, we apply two-dimensional Tikhonov Regularization (2DTR) to simulate subgrid surface patterns for ecological applications. Specifically, we test the ability of 2DTR to simulate the spatial statistics of high-resolution (4 m) remote sensing observations of the normalized difference vegetation index (NDVI) in a tundra landscape. We find that the 2DTR approach as applied here can capture the major mode of spatial variability of the high-resolution information, but not multiple modes of spatial variability, and that the Lagrange multiplier (γ) used to impose the condition of smoothness across space is related to the range of the experimental semivariogram. We used observed and 2DTR-simulated maps of NDVI to estimate landscape-level leaf area index (LAI) and gross primary productivity (GPP). NDVI maps simulated using a γ value that approximates the range of observed NDVI result in a landscape-level GPP estimate that differs by ca 2% from those created using observed NDVI. Following findings that GPP per unit LAI is lower near vegetation patch edges, we simulated vegetation patch edges using multiple approaches and found that simulated GPP declined by up to 12% as a result. 2DTR can generate random landscapes rapidly and can be applied to disaggregate ecological information and compare of spatial observations against simulated landscapes. PMID:26067835

  19. Multi-scale Characterization and Modeling of Surface Slope Probability Distribution for ~20-km Diameter Lunar Craters

    NASA Astrophysics Data System (ADS)

    Mahanti, P.; Robinson, M. S.; Boyd, A. K.

    2013-12-01

    Craters ~20-km diameter and above significantly shaped the lunar landscape. The statistical nature of the slope distribution on their walls and floors dominate the overall slope distribution statistics for the lunar surface. Slope statistics are inherently useful for characterizing the current topography of the surface, determining accurate photometric and surface scattering properties, and in defining lunar surface trafficability [1-4]. Earlier experimental studies on the statistical nature of lunar surface slopes were restricted either by resolution limits (Apollo era photogrammetric studies) or by model error considerations (photoclinometric and radar scattering studies) where the true nature of slope probability distribution was not discernible at baselines smaller than a kilometer[2,3,5]. Accordingly, historical modeling of lunar surface slopes probability distributions for applications such as in scattering theory development or rover traversability assessment is more general in nature (use of simple statistical models such as the Gaussian distribution[1,2,5,6]). With the advent of high resolution, high precision topographic models of the Moon[7,8], slopes in lunar craters can now be obtained at baselines as low as 6-meters allowing unprecedented multi-scale (multiple baselines) modeling possibilities for slope probability distributions. Topographic analysis (Lunar Reconnaissance Orbiter Camera (LROC) Narrow Angle Camera (NAC) 2-m digital elevation models (DEM)) of ~20-km diameter Copernican lunar craters revealed generally steep slopes on interior walls (30° to 36°, locally exceeding 40°) over 15-meter baselines[9]. In this work, we extend the analysis from a probability distribution modeling point-of-view with NAC DEMs to characterize the slope statistics for the floors and walls for the same ~20-km Copernican lunar craters. The difference in slope standard deviations between the Gaussian approximation and the actual distribution (2-meter sampling) was

  20. Using Multi-scale Modeling System to Study the Interactions between Clouds, Precipitation, Aerosols, Radiation and Land Surface

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo

    2006-01-01

    developments, improvements and applications of cloud models (GCE and WRF) at Goddard will be presented in this talk. In particular, a new approach to using multi-scale modeling system to study the interactions between clouds, precipitation, aerosols and land will be presented.

  1. Using Multi-scale Modeling System to Study the Interactions between Clouds, Precipitation, Aerosols, Radiation and Land Surface

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo

    2006-01-01

    technique. A review of developments, improvements and applications of cloud models (GCE and WRF) at Goddard wlll be is presented in this talk. In particular, a new approach to using multi-scale modeling system to study the interactions between clouds, precipitation, aerosols and land will be presented.

  2. Using Multi-scale Modeling System to Study the Interactions between Clouds, Precipitation, Aerosols, Radiation and Land Surface

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo

    2006-01-01

    nesting technique. A review of developments, improvements and applications of cloud models (GCE and WRF) at Goddard will be presented in this talk. In particular, a new approach to using multi-scale modeling system to study the interactions between clouds, precipitation, aerosols and land will be presented.

  3. Multi-scale computational models of the airways to unravel the pathophysiological mechanisms in asthma and chronic obstructive pulmonary disease (AirPROM)

    PubMed Central

    Burrowes, K. S.; De Backer, J.; Smallwood, R.; Sterk, P. J.; Gut, I.; Wirix-Speetjens, R.; Siddiqui, S.; Owers-Bradley, J.; Wild, J.; Maier, D.; Brightling, C.

    2013-01-01

    The respiratory system comprises several scales of biological complexity: the genes, cells and tissues that work in concert to generate resultant function. Malfunctions of the structure or function of components at any spatial scale can result in diseases, to the detriment of gas exchange, right heart function and patient quality of life. Vast amounts of data emerge from studies across each of the biological scales; however, the question remains: how can we integrate and interpret these data in a meaningful way? Respiratory disease presents a huge health and economic burden, with the diseases asthma and chronic obstructive pulmonary disease (COPD) affecting over 500 million people worldwide. Current therapies are inadequate owing to our incomplete understanding of the disease pathophysiology and our lack of recognition of the enormous disease heterogeneity: we need to characterize this heterogeneity on a patient-specific basis to advance healthcare. In an effort to achieve this goal, the AirPROM consortium (Airway disease Predicting Outcomes through patient-specific computational Modelling) brings together a multi-disciplinary team and a wealth of clinical data. Together we are developing an integrated multi-scale model of the airways in order to unravel the complex pathophysiological mechanisms occurring in the diseases asthma and COPD. PMID:24427517

  4. Stochastic multi-scale models of competition within heterogeneous cellular populations: Simulation methods and mean-field analysis.

    PubMed

    Cruz, Roberto de la; Guerrero, Pilar; Spill, Fabian; Alarcón, Tomás

    2016-10-21

    We propose a modelling framework to analyse the stochastic behaviour of heterogeneous, multi-scale cellular populations. We illustrate our methodology with a particular example in which we study a population with an oxygen-regulated proliferation rate. Our formulation is based on an age-dependent stochastic process. Cells within the population are characterised by their age (i.e. time elapsed since they were born). The age-dependent (oxygen-regulated) birth rate is given by a stochastic model of oxygen-dependent cell cycle progression. Once the birth rate is determined, we formulate an age-dependent birth-and-death process, which dictates the time evolution of the cell population. The population is under a feedback loop which controls its steady state size (carrying capacity): cells consume oxygen which in turn fuels cell proliferation. We show that our stochastic model of cell cycle progression allows for heterogeneity within the cell population induced by stochastic effects. Such heterogeneous behaviour is reflected in variations in the proliferation rate. Within this set-up, we have established three main results. First, we have shown that the age to the G1/S transition, which essentially determines the birth rate, exhibits a remarkably simple scaling behaviour. Besides the fact that this simple behaviour emerges from a rather complex model, this allows for a huge simplification of our numerical methodology. A further result is the observation that heterogeneous populations undergo an internal process of quasi-neutral competition. Finally, we investigated the effects of cell-cycle-phase dependent therapies (such as radiation therapy) on heterogeneous populations. In particular, we have studied the case in which the population contains a quiescent sub-population. Our mean-field analysis and numerical simulations confirm that, if the survival fraction of the therapy is too high, rescue of the quiescent population occurs. This gives rise to emergence of resistance

  5. Uncertainty quantification of fast sodium current steady-state inactivation for multi-scale models of cardiac electrophysiology.

    PubMed

    Pathmanathan, Pras; Shotwell, Matthew S; Gavaghan, David J; Cordeiro, Jonathan M; Gray, Richard A

    2015-01-01

    Perhaps the most mature area of multi-scale systems biology is the modelling of the heart. Current models are grounded in over fifty years of research in the development of biophysically detailed models of the electrophysiology (EP) of cardiac cells, but one aspect which is inadequately addressed is the incorporation of uncertainty and physiological variability. Uncertainty quantification (UQ) is the identification and characterisation of the uncertainty in model parameters derived from experimental data, and the computation of the resultant uncertainty in model outputs. It is a necessary tool for establishing the credibility of computational models, and will likely be expected of EP models for future safety-critical clinical applications. The focus of this paper is formal UQ of one major sub-component of cardiac EP models, the steady-state inactivation of the fast sodium current, INa. To better capture average behaviour and quantify variability across cells, we have applied for the first time an 'individual-based' statistical methodology to assess voltage clamp data. Advantages of this approach over a more traditional 'population-averaged' approach are highlighted. The method was used to characterise variability amongst cells isolated from canine epi and endocardium, and this variability was then 'propagated forward' through a canine model to determine the resultant uncertainty in model predictions at different scales, such as of upstroke velocity and spiral wave dynamics. Statistically significant differences between epi and endocardial cells (greater half-inactivation and less steep slope of steady state inactivation curve for endo) was observed, and the forward propagation revealed a lack of robustness of the model to underlying variability, but also surprising robustness to variability at the tissue scale. Overall, the methodology can be used to: (i) better analyse voltage clamp data; (ii) characterise underlying population variability; (iii) investigate

  6. Uncertainty quantification of fast sodium current steady-state inactivation for multi-scale models of cardiac electrophysiology.

    PubMed

    Pathmanathan, Pras; Shotwell, Matthew S; Gavaghan, David J; Cordeiro, Jonathan M; Gray, Richard A

    2015-01-01

    Perhaps the most mature area of multi-scale systems biology is the modelling of the heart. Current models are grounded in over fifty years of research in the development of biophysically detailed models of the electrophysiology (EP) of cardiac cells, but one aspect which is inadequately addressed is the incorporation of uncertainty and physiological variability. Uncertainty quantification (UQ) is the identification and characterisation of the uncertainty in model parameters derived from experimental data, and the computation of the resultant uncertainty in model outputs. It is a necessary tool for establishing the credibility of computational models, and will likely be expected of EP models for future safety-critical clinical applications. The focus of this paper is formal UQ of one major sub-component of cardiac EP models, the steady-state inactivation of the fast sodium current, INa. To better capture average behaviour and quantify variability across cells, we have applied for the first time an 'individual-based' statistical methodology to assess voltage clamp data. Advantages of this approach over a more traditional 'population-averaged' approach are highlighted. The method was used to characterise variability amongst cells isolated from canine epi and endocardium, and this variability was then 'propagated forward' through a canine model to determine the resultant uncertainty in model predictions at different scales, such as of upstroke velocity and spiral wave dynamics. Statistically significant differences between epi and endocardial cells (greater half-inactivation and less steep slope of steady state inactivation curve for endo) was observed, and the forward propagation revealed a lack of robustness of the model to underlying variability, but also surprising robustness to variability at the tissue scale. Overall, the methodology can be used to: (i) better analyse voltage clamp data; (ii) characterise underlying population variability; (iii) investigate

  7. Multi-scale textural feature extraction and particle swarm optimization based model selection for false positive reduction in mammography.

    PubMed

    Zyout, Imad; Czajkowska, Joanna; Grzegorzek, Marcin

    2015-12-01

    The high number of false positives and the resulting number of avoidable breast biopsies are the major problems faced by current mammography Computer Aided Detection (CAD) systems. False positive reduction is not only a requirement for mass but also for calcification CAD systems which are currently deployed for clinical use. This paper tackles two problems related to reducing the number of false positives in the detection of all lesions and masses, respectively. Firstly, textural patterns of breast tissue have been analyzed using several multi-scale textural descriptors based on wavelet and gray level co-occurrence matrix. The second problem addressed in this paper is the parameter selection and performance optimization. For this, we adopt a model selection procedure based on Particle Swarm Optimization (PSO) for selecting the most discriminative textural features and for strengthening the generalization capacity of the supervised learning stage based on a Support Vector Machine (SVM) classifier. For evaluating the proposed methods, two sets of suspicious mammogram regions have been used. The first one, obtained from Digital Database for Screening Mammography (DDSM), contains 1494 regions (1000 normal and 494 abnormal samples). The second set of suspicious regions was obtained from database of Mammographic Image Analysis Society (mini-MIAS) and contains 315 (207 normal and 108 abnormal) samples. Results from both datasets demonstrate the efficiency of using PSO based model selection for optimizing both classifier hyper-parameters and parameters, respectively. Furthermore, the obtained results indicate the promising performance of the proposed textural features and more specifically, those based on co-occurrence matrix of wavelet image representation technique. PMID:25795630

  8. Multi-scale textural feature extraction and particle swarm optimization based model selection for false positive reduction in mammography.

    PubMed

    Zyout, Imad; Czajkowska, Joanna; Grzegorzek, Marcin

    2015-12-01

    The high number of false positives and the resulting number of avoidable breast biopsies are the major problems faced by current mammography Computer Aided Detection (CAD) systems. False positive reduction is not only a requirement for mass but also for calcification CAD systems which are currently deployed for clinical use. This paper tackles two problems related to reducing the number of false positives in the detection of all lesions and masses, respectively. Firstly, textural patterns of breast tissue have been analyzed using several multi-scale textural descriptors based on wavelet and gray level co-occurrence matrix. The second problem addressed in this paper is the parameter selection and performance optimization. For this, we adopt a model selection procedure based on Particle Swarm Optimization (PSO) for selecting the most discriminative textural features and for strengthening the generalization capacity of the supervised learning stage based on a Support Vector Machine (SVM) classifier. For evaluating the proposed methods, two sets of suspicious mammogram regions have been used. The first one, obtained from Digital Database for Screening Mammography (DDSM), contains 1494 regions (1000 normal and 494 abnormal samples). The second set of suspicious regions was obtained from database of Mammographic Image Analysis Society (mini-MIAS) and contains 315 (207 normal and 108 abnormal) samples. Results from both datasets demonstrate the efficiency of using PSO based model selection for optimizing both classifier hyper-parameters and parameters, respectively. Furthermore, the obtained results indicate the promising performance of the proposed textural features and more specifically, those based on co-occurrence matrix of wavelet image representation technique.

  9. Multi-scale continuum modeling of biological processes: from molecular electro-diffusion to sub-cellular signaling transduction

    NASA Astrophysics Data System (ADS)

    Cheng, Y.; Kekenes-Huskey, P.; Hake, J. E.; Holst, M. J.; McCammon, J. A.; Michailova, A. P.

    2012-01-01

    This paper presents a brief review of multi-scale modeling at the molecular to cellular scale, with new results for heart muscle cells. A finite element-based simulation package (SMOL) was used to investigate the signaling transduction at molecular and sub-cellular scales (http://mccammon.ucsd.edu/smol/, http://FETK.org) by numerical solution of the time-dependent Smoluchowski equations and a reaction-diffusion system. At the molecular scale, SMOL has yielded experimentally validated estimates of the diffusion-limited association rates for the binding of acetylcholine to mouse acetylcholinesterase using crystallographic structural data. The predicted rate constants exhibit increasingly delayed steady-state times, with increasing ionic strength, and demonstrate the role of an enzyme's electrostatic potential in influencing ligand binding. At the sub-cellular scale, an extension of SMOL solves a nonlinear, reaction-diffusion system describing Ca2+ ligand buffering and diffusion in experimentally derived rodent ventricular myocyte geometries. Results reveal the important role of mobile and stationary Ca2+ buffers, including Ca2+ indicator dye. We found that alterations in Ca2+-binding and dissociation rates of troponin C (TnC) and total TnC concentration modulate sub-cellular Ca2+ signals. The model predicts that reduced off-rate in the whole troponin complex (TnC, TnI, TnT) versus reconstructed thin filaments (Tn, Tm, actin) alters cytosolic Ca2+ dynamics under control conditions or in disease-linked TnC mutations. The ultimate goal of these studies is to develop scalable methods and theories for the integration of molecular-scale information into simulations of cellular-scale systems.

  10. Development of a kinetic particle-based method to model the multi-scale physics of expanding flows

    NASA Astrophysics Data System (ADS)

    Kumar, Rakesh

    Multi-scale transitional flows through a nozzle into vacuum are widely studied flows because of their numerous applications in many fields of science and engineering, and, especially in aerospace sciences. These flows are usually characterized by multiple flow length scales, which significantly complicate their accurate and numerically efficient modeling. Experimental studies under such conditions are rare and expensive. For both micro and meso-sized nozzles operating in the space near-vacuum environment, the interaction of flows with sensitive spacecraft surfaces at high altitudes is important, because back-flows produced by such devices can cause contamination to sensitive electronic devices such as optical instruments and solar panels. This damage can potentially jeopardize the active lifetime of expensive space missions. The development of accurate numerical tools capable of simulating multi-scale transitional flows is therefore important, but at the same time, challenging, because the flow regime changes from continuum to transitional along the length of the domain. The continuum techniques based on the solution of the Navier-Stokes equations encounter physical challenges when applied to these flows. In such a scenario, the study of high speed rarefied flows, involving strong thermo-chemical non-equilibrium, suggests direct consideration of the Boltzmann equation. The Direct Simulation Monte-Carlo (DSMC) approach provides a good approximation to the solution of the Boltzmann equation, but the method becomes prohibitively expensive for modeling high density flows. The Bhatnagar-Gross-Krook (BGK) method, which solves a simplified form of the Boltzmann equation, is more effective approach in such situations. A computational framework based on a statistical formulation of the BGK method was therefore developed in this work that can handle polyatomic multi-species gas flows. A number of classic fluid flow problems in semi-rarefied flow regime were studied to

  11. A Combined In Vitro Imaging and Multi-Scale Modeling System for Studying the Role of Cell Matrix Interactions in Cutaneous Wound Healing.

    PubMed

    De Jesus, Aribet M; Aghvami, Maziar; Sander, Edward A

    2016-01-01

    Many cell types remodel the extracellular matrix of the tissues they inhabit in response to a wide range of environmental stimuli, including mechanical cues. Such is the case in dermal wound healing, where fibroblast migrate into and remodel the provisional fibrin matrix in a complex manner that depends in part on the local mechanical environment and the evolving multi-scale mechanical interactions of the system. In this study, we report on the development of an image-based multi-scale mechanical model that predicts the short-term (24 hours), structural reorganization of a fibrin gel by fibroblasts. These predictive models are based on an in vitro experimental system where clusters of fibroblasts (i.e., explants) were spatially arranged into a triangular geometry onto the surface of fibrin gels that were subjected to either Fixed or Free in-plane mechanical constraints. Experimentally, regional differences in short-term structural remodeling and cell migration were observed for the two gel boundary conditions. A pilot experiment indicated that these small differences in the short-term remodeling of the fibrin gel translate into substantial differences in long-term (4 weeks) remodeling, particularly in terms of collagen production. The multi-scale models were able to predict some regional differences in remodeling and qualitatively similar reorganization patterns for the two boundary conditions. However, other aspects of the model, such as the magnitudes and rates of deformation of gel, did not match the experiments. These discrepancies between model and experiment provide fertile ground for challenging model assumptions and devising new experiments to enhance our understanding of how this multi-scale system functions. These efforts will ultimately improve the predictions of the remodeling process, particularly as it relates to dermal wound healing and the reduction of patient scarring. Such models could be used to recommend patient-specific mechanical

  12. A Combined In Vitro Imaging and Multi-Scale Modeling System for Studying the Role of Cell Matrix Interactions in Cutaneous Wound Healing

    PubMed Central

    2016-01-01

    Many cell types remodel the extracellular matrix of the tissues they inhabit in response to a wide range of environmental stimuli, including mechanical cues. Such is the case in dermal wound healing, where fibroblast migrate into and remodel the provisional fibrin matrix in a complex manner that depends in part on the local mechanical environment and the evolving multi-scale mechanical interactions of the system. In this study, we report on the development of an image-based multi-scale mechanical model that predicts the short-term (24 hours), structural reorganization of a fibrin gel by fibroblasts. These predictive models are based on an in vitro experimental system where clusters of fibroblasts (i.e., explants) were spatially arranged into a triangular geometry onto the surface of fibrin gels that were subjected to either Fixed or Free in-plane mechanical constraints. Experimentally, regional differences in short-term structural remodeling and cell migration were observed for the two gel boundary conditions. A pilot experiment indicated that these small differences in the short-term remodeling of the fibrin gel translate into substantial differences in long-term (4 weeks) remodeling, particularly in terms of collagen production. The multi-scale models were able to predict some regional differences in remodeling and qualitatively similar reorganization patterns for the two boundary conditions. However, other aspects of the model, such as the magnitudes and rates of deformation of gel, did not match the experiments. These discrepancies between model and experiment provide fertile ground for challenging model assumptions and devising new experiments to enhance our understanding of how this multi-scale system functions. These efforts will ultimately improve the predictions of the remodeling process, particularly as it relates to dermal wound healing and the reduction of patient scarring. Such models could be used to recommend patient-specific mechanical

  13. Resolving the Multi-scale Behavior of Geochemical Weathering in the Critical Zone Using High Resolution Hydro-geochemical Models

    NASA Astrophysics Data System (ADS)

    Pandey, S.; Rajaram, H.

    2015-12-01

    This work investigates hydrologic and geochemical interactions in the Critical Zone (CZ) using high-resolution reactive transport modeling. Reactive transport models can be used to predict the response of geochemical weathering and solute fluxes in the CZ to changes in a dynamic environment, such as those pertaining to human activities and climate change in recent years. The scales of hydrology and geochemistry in the CZ range from days to eons in time and centimeters to kilometers in space. Here, we present results of a multi-dimensional, multi-scale hydro-geochemical model to investigate the role of subsurface heterogeneity on the formation of mineral weathering fronts in the CZ, which requires consideration of many of these spatio-temporal scales. The model is implemented using the reactive transport code PFLOTRAN, an open source subsurface flow and reactive transport code that utilizes parallelization over multiple processing nodes and provides a strong framework for simulating weathering in the CZ. The model is set up to simulate weathering dynamics in the mountainous catchments representative of the Colorado Front Range. Model parameters were constrained based on hydrologic, geochemical, and geophysical observations from the Boulder Creek Critical Zone Observatory (BcCZO). Simulations were performed in fractured rock systems and compared with systems of heterogeneous and homogeneous permeability fields. Tracer simulations revealed that the mean residence time of solutes was drastically accelerated as fracture density increased. In simulations that include mineral reactions, distinct signatures of transport limitations on weathering arose when discrete flow paths were included. This transport limitation was related to both advective and diffusive processes in the highly heterogeneous systems (i.e. fractured media and correlated random permeability fields with σlnk > 3). The well-known time-dependence of mineral weathering rates was found to be the most

  14. Damage and failure modelling of hybrid three-dimensional textile composites: a mesh objective multi-scale approach.

    PubMed

    Patel, Deepak K; Waas, Anthony M

    2016-07-13

    -induced geometric imperfections are included in the simulation, where the FE mesh of the unit cell is generated directly from micro-computed tomography (MCT) real data using a code Simpleware Results from multi-scale analysis for both an idealized perfect geometry and one that includes geometric imperfections are compared with experimental results (Pankow et al. 2012 53rd AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics and Materials Conference, Honolulu, HI, 23-26 April 2012 AIAA 2012-1572). This article is part of the themed issue 'Multiscale modelling of the structural integrity of composite materials'.

  15. Damage and failure modelling of hybrid three-dimensional textile composites: a mesh objective multi-scale approach.

    PubMed

    Patel, Deepak K; Waas, Anthony M

    2016-07-13

    -induced geometric imperfections are included in the simulation, where the FE mesh of the unit cell is generated directly from micro-computed tomography (MCT) real data using a code Simpleware Results from multi-scale analysis for both an idealized perfect geometry and one that includes geometric imperfections are compared with experimental results (Pankow et al. 2012 53rd AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics and Materials Conference, Honolulu, HI, 23-26 April 2012 AIAA 2012-1572). This article is part of the themed issue 'Multiscale modelling of the structural integrity of composite materials'. PMID:27242294

  16. Toward Improving Predictability of Extreme Hydrometeorological Events: the Use of Multi-scale Climate Modeling in the Northern High Plains

    NASA Astrophysics Data System (ADS)

    Munoz-Arriola, F.; Torres-Alavez, J.; Mohamad Abadi, A.; Walko, R. L.

    2014-12-01

    Our goal is to investigate possible sources of predictability of hydrometeorological extreme events in the Northern High Plains. Hydrometeorological extreme events are considered the most costly natural phenomena. Water deficits and surpluses highlight how the water-climate interdependence becomes crucial in areas where single activities drive economies such as Agriculture in the NHP. Nonetheless we recognize the Water-Climate interdependence and the regulatory role that human activities play, we still grapple to identify what sources of predictability could be added to flood and drought forecasts. To identify the benefit of multi-scale climate modeling and the role of initial conditions on flood and drought predictability on the NHP, we use the Ocean Land Atmospheric Model (OLAM). OLAM is characterized by a dynamic core with a global geodesic grid with hexagonal (and variably refined) mesh cells and a finite volume discretization of the full compressible Navier Stokes equations, a cut-grid cell method for topography (that reduces error in computational gradient computation and anomalous vertical dispersion). Our hypothesis is that wet conditions will drive OLAM's simulations of precipitation to wetter conditions affecting both flood forecast and drought forecast. To test this hypothesis we simulate precipitation during identified historical flood events followed by drought events in the NHP (i.e. 2011-2012 years). We initialized OLAM with CFS-data 1-10 days previous to a flooding event (as initial conditions) to explore (1) short-term and high-resolution and (2) long-term and coarse-resolution simulations of flood and drought events, respectively. While floods are assessed during a maximum of 15-days refined-mesh simulations, drought is evaluated during the following 15 months. Simulated precipitation will be compared with the Sub-continental Observation Dataset, a gridded 1/16th degree resolution data obtained from climatological stations in Canada, US, and

  17. Quantifying restoration effectiveness using multi-scale habitat models: implications for sage-grouse in the Great Basin

    USGS Publications Warehouse

    Arkle, Robert S.; Pilliod, David S.; Hanser, Steven E.; Brooks, Matthew L.; Chambers, Jeanne C.; Grace, James B.; Knutson, Kevin C.; Pyke, David A.; Welty, Justin L.

    2014-01-01

    A recurrent challenge in the conservation of wide-ranging, imperiled species is understanding which habitats to protect and whether we are capable of restoring degraded landscapes. For Greater Sage-grouse (Centrocercus urophasianus), a species of conservation concern in the western United States, we approached this problem by developing multi-scale empirical models of occupancy in 211 randomly located plots within a 40 million ha portion of the species' range. We then used these models to predict sage-grouse habitat quality at 826 plots associated with 101 post-wildfire seeding projects implemented from 1990 to 2003. We also compared conditions at restoration sites to published habitat guidelines. Sage-grouse occupancy was positively related to plot- and landscape-level dwarf sagebrush (Artemisia arbuscula, A. nova, A. tripartita) and big sagebrush steppe prevalence, and negatively associated with non-native plants and human development. The predicted probability of sage-grouse occupancy at treated plots was low on average (0.09) and not substantially different from burned areas that had not been treated. Restoration sites with quality habitat tended to occur at higher elevation locations with low annual temperatures, high spring precipitation, and high plant diversity. Of 313 plots seeded after fire, none met all sagebrush guidelines for breeding habitats, but approximately 50% met understory guidelines, particularly for perennial grasses. This pattern was similar for summer habitat. Less than 2% of treated plots met winter habitat guidelines. Restoration actions did not increase the probability of burned areas meeting most guideline criteria. The probability of meeting guidelines was influenced by a latitudinal gradient, climate, and topography. Our results suggest that sage-grouse are relatively unlikely to use many burned areas within 20 years of fire, regardless of treatment. Understory habitat conditions are more likely to be adequate than overstory

  18. Multi-scale 3D X-ray Imaging Capabilities at the Advanced Photon Source - Current status and future direction (Invited)

    NASA Astrophysics Data System (ADS)

    DeCarlo, F.; Xiao, X.; Khan, F.; Glowacki, A.; Schwarz, N.; Jacobsen, C.

    2013-12-01

    In x-ray computed μ-tomography (μ-XCT), a thin scintillator screen is coupled to a visible light lens and camera system to obtain micrometer-scale transmission imaging of specimens as large as a few millimeters. Recent advances in detector technology allow collecting these images at unprecedented frame rates. For a high x-ray flux density synchrotron facility like the Advanced Photon Source (APS), the detector exposure time ranges from hundreds of milliseconds to hundreds of picoseconds, making possible to acquire a full 3D micrometer-resolution dataset in less than one second. The micron resolution limitation of parallel x-ray beam projection systems can be overcame by Transmission X-ray Microscopes (TXM) where part of the image magnification is done in x-ray regime using x-ray optics like capillary condensers and Fresnel zone plates. These systems, when installed on a synchrotron x-ray source, can generate 2D images with up to 20 nm resolution with second exposure time and collect a full 3D nano-resolution dataset in few minutes. μ-XCT and TXM systems available at the x-ray imaging beamlines of the APS are routinely used in material science and geoscience applications where high-resolution and fast 3D imaging are instrumental in extracting in situ four-dimensional dynamic information. In this presentation we describe the computational challenges associated with μ-XCT and TXM systems and present the framework and infrastructure developed at the APS to allow for routine multi-scale data integration between the two systems.

  19. Multi-scale 3D X-ray Imaging Capabilities at the Advanced Photon Source - Current status and future direction (Invited)

    NASA Astrophysics Data System (ADS)

    DeCarlo, F.; Xiao, X.; Khan, F.; Glowacki, A.; Schwarz, N.; Jacobsen, C.

    2011-12-01

    In x-ray computed μ-tomography (μ-XCT), a thin scintillator screen is coupled to a visible light lens and camera system to obtain micrometer-scale transmission imaging of specimens as large as a few millimeters. Recent advances in detector technology allow collecting these images at unprecedented frame rates. For a high x-ray flux density synchrotron facility like the Advanced Photon Source (APS), the detector exposure time ranges from hundreds of milliseconds to hundreds of picoseconds, making possible to acquire a full 3D micrometer-resolution dataset in less than one second. The micron resolution limitation of parallel x-ray beam projection systems can be overcame by Transmission X-ray Microscopes (TXM) where part of the image magnification is done in x-ray regime using x-ray optics like capillary condensers and Fresnel zone plates. These systems, when installed on a synchrotron x-ray source, can generate 2D images with up to 20 nm resolution with second exposure time and collect a full 3D nano-resolution dataset in few minutes. μ-XCT and TXM systems available at the x-ray imaging beamlines of the APS are routinely used in material science and geoscience applications where high-resolution and fast 3D imaging are instrumental in extracting in situ four-dimensional dynamic information. In this presentation we describe the computational challenges associated with μ-XCT and TXM systems and present the framework and infrastructure developed at the APS to allow for routine multi-scale data integration between the two systems.

  20. Multi-scale approach to the modeling of fission gas discharge during hypothetical loss-of-flow accident in gen-IV sodium fast reactor

    SciTech Connect

    Behafarid, F.; Shaver, D. R.; Bolotnov, I. A.; Jansen, K. E.; Antal, S. P.; Podowski, M. Z.

    2012-07-01

    The required technological and safety standards for future Gen IV Reactors can only be achieved if advanced simulation capabilities become available, which combine high performance computing with the necessary level of modeling detail and high accuracy of predictions. The purpose of this paper is to present new results of multi-scale three-dimensional (3D) simulations of the inter-related phenomena, which occur as a result of fuel element heat-up and cladding failure, including the injection of a jet of gaseous fission products into a partially blocked Sodium Fast Reactor (SFR) coolant channel, and gas/molten sodium transport along the coolant channels. The computational approach to the analysis of the overall accident scenario is based on using two different inter-communicating computational multiphase fluid dynamics (CMFD) codes: a CFD code, PHASTA, and a RANS code, NPHASE-CMFD. Using the geometry and time history of cladding failure and the gas injection rate, direct numerical simulations (DNS), combined with the Level Set method, of two-phase turbulent flow have been performed by the PHASTA code. The model allows one to track the evolution of gas/liquid interfaces at a centimeter scale. The simulated phenomena include the formation and breakup of the jet of fission products injected into the liquid sodium coolant. The PHASTA outflow has been averaged over time to obtain mean phasic velocities and volumetric concentrations, as well as the liquid turbulent kinetic energy and turbulence dissipation rate, all of which have served as the input to the core-scale simulations using the NPHASE-CMFD code. A sliding window time averaging has been used to capture mean flow parameters for transient cases. The results presented in the paper include testing and validation of the proposed models, as well the predictions of fission-gas/liquid-sodium transport along a multi-rod fuel assembly of SFR during a partial loss-of-flow accident. (authors)

  1. Unified Modeling Language description of the object-oriented multi-scale adaptive finite element method for Step-and-Flash Imprint Lithography Simulations

    NASA Astrophysics Data System (ADS)

    Paszyński, Maciej; Gurgul, Piotr; Sieniek, Marcin; Pardo, David

    2010-06-01

    In the first part of the paper we present the multi-scale simulation of the Step-and-Flash Imprint Lithography (SFIL), a modern patterning process. The simulation utilizes the hp adaptive Finite Element Method (hp-FEM) coupled with Molecular Statics (MS) model. Thus, we consider the multi-scale problem, with molecular statics applied in the areas of the mesh where the highest accuracy is required, and the continuous linear elasticity with thermal expansion coefficient applied in the remaining part of the domain. The degrees of freedom from macro-scale element's nodes located on the macro-scale side of the interface have been identified with particles from nano-scale elements located on the nano-scale side of the interface. In the second part of the paper we present Unified Modeling Language (UML) description of the resulting multi-scale application (hp-FEM coupled with MS). We investigated classical, procedural codes from the point of view of the object-oriented (O-O) programming paradigm. The discovered hierarchical structure of classes and algorithms makes the UML project as independent on the spatial dimension of the problem as possible. The O-O UML project was defined at an abstract level, independent on the programming language used.

  2. Viscoelastic Model for Lung Parenchyma for Multi-Scale Modeling of Respiratory System, Phase II: Dodecahedral Micro-Model

    SciTech Connect

    Freed, Alan D.; Einstein, Daniel R.; Carson, James P.; Jacob, Rick E.

    2012-03-01

    In the first year of this contractual effort a hypo-elastic constitutive model was developed and shown to have great potential in modeling the elastic response of parenchyma. This model resides at the macroscopic level of the continuum. In this, the second year of our support, an isotropic dodecahedron is employed as an alveolar model. This is a microscopic model for parenchyma. A hopeful outcome is that the linkage between these two scales of modeling will be a source of insight and inspiration that will aid us in the final year's activity: creating a viscoelastic model for parenchyma.

  3. MATCH-SALSA - Multi-scale Atmospheric Transport and CHemistry model coupled to the SALSA aerosol microphysics model - Part 1: Model description and evaluation

    NASA Astrophysics Data System (ADS)

    Andersson, C.; Bergström, R.; Bennet, C.; Robertson, L.; Thomas, M.; Korhonen, H.; Lehtinen, K. E. J.; Kokkola, H.

    2014-05-01

    We have implemented the sectional aerosol dynamics model SALSA in the European scale chemistry-transport model MATCH (Multi-scale Atmospheric Transport and Chemistry). The new model is called MATCH-SALSA. It includes aerosol microphysics, with several formulations for nucleation, wet scavenging and condensation. The model reproduces observed higher particle number concentration (PNC) in central Europe and lower concentrations in remote regions. The model PNC size distribution peak occurs at the same or smaller particle size as the observed peak at five measurement sites spread across Europe. Total PNC is underestimated at Northern and Central European sites and accumulation mode PNC is underestimated at all investigated sites. On the other hand the model performs well for particle mass, including secondary inorganic aerosol components. Elemental and organic carbon concentrations are underestimated at many of the sites. Further development is needed, primarily for treatment of secondary organic aerosol, both in terms of biogenic emissions and chemical transformation, and for nitrogen gas-particle partitioning. Updating the biogenic SOA scheme will likely have a large impact on modeled PM2.5 and also affect the model performance for PNC through impacts on nucleation and condensation. An improved nitrogen partitioning model may also improve the description of condensational growth.

  4. MATCH-SALSA - Multi-scale Atmospheric Transport and CHemistry model coupled to the SALSA aerosol microphysics model - Part 1: Model description and evaluation

    NASA Astrophysics Data System (ADS)

    Andersson, C.; Bergström, R.; Bennet, C.; Robertson, L.; Thomas, M.; Korhonen, H.; Lehtinen, K. E. J.; Kokkola, H.

    2015-02-01

    We have implemented the sectional aerosol dynamics model SALSA (Sectional Aerosol module for Large Scale Applications) in the European-scale chemistry-transport model MATCH (Multi-scale Atmospheric Transport and Chemistry). The new model is called MATCH-SALSA. It includes aerosol microphysics, with several formulations for nucleation, wet scavenging and condensation. The model reproduces observed higher particle number concentration (PNC) in central Europe and lower concentrations in remote regions. The modeled PNC size distribution peak occurs at the same or smaller particle size as the observed peak at four measurement sites spread across Europe. Total PNC is underestimated at northern and central European sites and accumulation-mode PNC is underestimated at all investigated sites. The low nucleation rate coefficient used in this study is an important reason for the underestimation. On the other hand, the model performs well for particle mass (including secondary inorganic aerosol components), while elemental and organic carbon concentrations are underestimated at many of the sites. Further development is needed, primarily for treatment of secondary organic aerosol, in terms of biogenic emissions and chemical transformation. Updating the biogenic secondary organic aerosol (SOA) scheme will likely have a large impact on modeled PM2.5 and also affect the model performance for PNC through impacts on nucleation and condensation.

  5. Multi-scale Measurements and Modeling to Verify and Attribute Carbon Dioxide Emissions from Four Corners Power Plants

    NASA Astrophysics Data System (ADS)

    Dubey, M. K.; Love, S. P.; Henderson, B. G.; Lee, S.; Costigan, K. R.; Reisner, J.; Flowers, B. A.; Chylek, P.

    2011-12-01

    inventories like Vulcan. WRF-Chem employs multiple nested grids and high resolution topography to simulate atmospheric variability ranging from synoptic scales to micro-scales (~200 m), while including locally developed flows influenced by the nearby complex terrain of the San Juan Mountains. The simulated local atmospheric dynamics are provided to force the HIGRAD plume model, which links meso-scale atmospheric variability to the small-scale simulation of the power plant plumes (~10m). Our multi-scale forward modeling simulations are compared with our column and in situ observations of CO2, other greenhouse gases and pollutants for specific days. We use this to quantify the current ability of remote and in situ sensing measurements to quantify emissions in a relatively simple environment. Finally, we examine satellite data (CO2 and CH4 from GOSAT and NO2 from OMI) for signals over Four Corners and assess the value added for longer-term trend analysis. We gratefully acknowledge members of the TCCON (D. Wunch and P. Wennberg) and HIPPO (S. Wofsy and B. Stephens) teams for their input and guidance.

  6. Multi-scale analysis of an electrochemical model including coupled diffusion, stress, and nonideal solution in a silicon thin film anode

    NASA Astrophysics Data System (ADS)

    Gwak, Yunki; Moon, Janghyuk; Cho, Maenghyo

    2016-03-01

    The electrochemical performance of Li-ion batteries strongly depends on the interaction between atomic scale and micro scale phenomena in high capacity electrode materials such as silicon and sulfur. Local thermodynamic interactions between host and guest species on atomic-scale significantly influence transfer kinetics and deformation kinematics on the micro-scale. We propose a multi-scale model to characterize the electrochemical and mechanical response of an amorphous silicon thin film during discharge/charge cycling. In the atomic-scale simulation, the stress-dependent energy barrier for the migration of lithium and the molar excess Gibbs free energy were calculated using density functional theory. These atomic-scale effects account for the nonlinear lithium diffusion behavior in the continuum simulation. In the continuum simulation, we considered the coupled diffusion and large deformation model on the cell-scale to determine the non-equilibrium cell potential as a function of the surface lithium concentration using Butler-Volmer kinetics. We clearly show that Li macroscopic kinetics is significantly affected by the stress induced by the volumetric strain associated with diffusion and the mixing formation energy of LixSi. Our simulation results demonstrate that the multi-scale model is consistent with experimental observations at different C-rates.

  7. Corrosion chemistry closing comments: opportunities in corrosion science facilitated by operando experimental characterization combined with multi-scale computational modelling.

    PubMed

    Scully, John R

    2015-01-01

    Recent advances in characterization tools, computational capabilities, and theories have created opportunities for advancement in understanding of solid-fluid interfaces at the nanoscale in corroding metallic systems. The Faraday Discussion on Corrosion Chemistry in 2015 highlighted some of the current needs, gaps and opportunities in corrosion science. Themes were organized into several hierarchical categories that provide an organizational framework for corrosion. Opportunities to develop fundamental physical and chemical data which will enable further progress in thermodynamic and kinetic modelling of corrosion were discussed. These will enable new and better understanding of unit processes that govern corrosion at the nanoscale. Additional topics discussed included scales, films and oxides, fluid-surface and molecular-surface interactions, selected topics in corrosion science and engineering as well as corrosion control. Corrosion science and engineering topics included complex alloy dissolution, local corrosion, and modelling of specific corrosion processes that are made up of collections of temporally and spatially varying unit processes such as oxidation, ion transport, and competitive adsorption. Corrosion control and mitigation topics covered some new insights on coatings and inhibitors. Further advances in operando or in situ experimental characterization strategies at the nanoscale combined with computational modelling will enhance progress in the field, especially if coupling across length and time scales can be achieved incorporating the various phenomena encountered in corrosion. Readers are encouraged to not only to use this ad hoc organizational scheme to guide their immersion into the current opportunities in corrosion chemistry, but also to find value in the information presented in their own ways.

  8. A Semi-Empirical Multi-Scale Dynamic Monte Carlo Model of Organic Photovoltaic Performance in RIR-MAPLE Bulk Heterojunction Films

    NASA Astrophysics Data System (ADS)

    Stiff-Roberts, Adrienne; Atewologun, Ayomide

    A semi-empirical method for investigating the performance of OPVs in resonant infrared, matrix-assisted pulsed laser evaporation (RIR-MAPLE) films is explored. Emulsion-based RIR-MAPLE offers a unique experimental backdrop for investigating trends through simulation and gaining a better understanding of how different thin film characteristics impact OPV device performance. A novel multi-scale formulation of the Dynamic Monte Carlo (DMC) model is developed based on observable morphology features. Specifically, using confocal microscopy, we observe the presence of micro-scale regimes of pure materials and nano-scale regions of the composite blend. This enables us to assign weighted percentages to DMC implementations on two different scales: the microscale and nanoscale regions. In addition to this, we use input simulation parameters acquired by characterization of as-deposited films. The semi-empirical multi-scale model presented serves as a unique simulation opportunity for exploring different properties of RIR-MAPLE deposited OPVs, their effects on OPV performance and potential design routes for improving device efficiencies. This work was supported, in part, by the Office of Naval Research under Grant N00014-10-1-0481 and the NSF Triangle MRSEC on Soft Matter.

  9. A multi-scale model of the interplay between cell signalling and hormone transport in specifying the root meristem of Arabidopsis thaliana.

    PubMed

    Muraro, D; Larrieu, A; Lucas, M; Chopard, J; Byrne, H; Godin, C; King, J

    2016-09-01

    The growth of the root of Arabidopsis thaliana is sustained by the meristem, a region of cell proliferation and differentiation which is located in the root apex and generates cells which move shootwards, expanding rapidly to cause root growth. The balance between cell division and differentiation is maintained via a signalling network, primarily coordinated by the hormones auxin, cytokinin and gibberellin. Since these hormones interact at different levels of spatial organisation, we develop a multi-scale computational model which enables us to study the interplay between these signalling networks and cell-cell communication during the specification of the root meristem. We investigate the responses of our model to hormonal perturbations, validating the results of our simulations against experimental data. Our simulations suggest that one or more additional components are needed to explain the observed expression patterns of a regulator of cytokinin signalling, ARR1, in roots not producing gibberellin. By searching for novel network components, we identify two mutant lines that affect significantly both root length and meristem size, one of which also differentially expresses a central component of the interaction network (SHY2). More generally, our study demonstrates how a multi-scale investigation can provide valuable insight into the spatio-temporal dynamics of signalling networks in biological tissues. PMID:27157127

  10. On the impact of modelling assumptions in multi-scale, subject-specific models of aortic haemodynamics

    PubMed Central

    Xiao, Nan; Fok, Henry; Schaeffter, Tobias; Figueroa, C. Alberto

    2016-01-01

    Simulation of haemodynamics has become increasingly popular within the research community. Irrespective of the modelling approach (zero-dimensional (0D), one-dimensional (1D) or three-dimensional (3D)), in vivo measurements are required to personalize the arterial geometry, material properties and boundary conditions of the computational model. Limitations in in vivo data acquisition often result in insufficient information to determine all model parameters and, hence, arbitrary modelling assumptions. Our goal was to minimize and understand the impact of modelling assumptions on the simulated blood pressure, flow and luminal area waveforms by studying a small region of the systemic vasculature—the upper aorta—and acquiring a rich array of non-invasive magnetic resonance imaging and tonometry data from a young healthy volunteer. We first investigated the effect of different modelling assumptions for boundary conditions and material parameters in a 1D/0D simulation framework. Strategies were implemented to mitigate the impact of inconsistencies in the in vivo data. Average relative errors smaller than 7% were achieved between simulated and in vivo waveforms. Similar results were obtained in a 3D/0D simulation framework using the same inflow and outflow boundary conditions and consistent geometrical and mechanical properties. We demonstrated that accurate subject-specific 1D/0D and 3D/0D models of aortic haemodynamics can be obtained using non-invasive clinical data while minimizing the number of arbitrary modelling decisions. PMID:27307511

  11. From systems biology to photosynthesis and whole-plant modeling: a conceptual model for integrating multi-scale networks

    SciTech Connect

    Weston, David; Hanson, Paul J; Norby, Richard J; Tuskan, Gerald A; Wullschleger, Stan D

    2012-01-01

    Network analysis is now a common statistical tool for molecular biologists. Network algorithms are readily used to model gene, protein and metabolic correlations providing insight into pathways driving biological phenomenon. One output from such an analysis is a candidate gene list that can be responsible, in part, for the biological process of interest. The question remains, however, as to whether molecular network analysis can be used to inform process models at higher levels of biological organization. In our previous work, transcriptional networks derived from three plant species were constructed, interrogated for orthology and then correlated to photosynthetic inhibition at elevated temperature. One unique aspect of that study was the link from co-expression networks to net photosynthesis. In this addendum, we propose a conceptual model where traditional network analysis can be linked to whole-plant models thereby informing predictions on key processes such as photosynthesis, nutrient uptake and assimilation, and C partitioning.

  12. The air quality forecast in Beijing with Community Multi-scale Air Quality Modeling (CMAQ) System: model evaluation and improvement

    NASA Astrophysics Data System (ADS)

    Wu, Q.

    2013-12-01

    The MM5-SMOKE-CMAQ model system, which is developed by the United States Environmental Protection Agency(U.S. EPA) as the Models-3 system, has been used for the daily air quality forecast in the Beijing Municipal Environmental Monitoring Center(Beijing MEMC), as a part of the Ensemble Air Quality Forecast System for Beijing(EMS-Beijing) since the Olympic Games year 2008. In this study, we collect the daily forecast results of the CMAQ model in the whole year 2010 for the model evaluation. The results show that the model play a good model performance in most days but underestimate obviously in some air pollution episode. A typical air pollution episode from 11st - 20th January 2010 was chosen, which the air pollution index(API) of particulate matter (PM10) observed by Beijing MEMC reaches to 180 while the prediction of PM10-API is about 100. Taking in account all stations in Beijing, including urban and suburban stations, three numerical methods are used for model improvement: firstly, enhance the inner domain with 4km grids, the coverage from only Beijing to the area including its surrounding cities; secondly, update the Beijing stationary area emission inventory, from statistical county-level to village-town level, that would provide more detail spatial informance for area emissions; thirdly, add some industrial points emission in Beijing's surrounding cities, the latter two are both the improvement of emission. As the result, the peak of the nine national standard stations averaged PM10-API, which is simulated by CMAQ as daily hindcast PM10-API, reach to 160 and much near to the observation. The new results show better model performance, which the correlation coefficent is 0.93 in national standard stations average and 0.84 in all stations, the relative error is 15.7% in national standard stations averaged and 27% in all stations. The time series of 9 national standard in Beijing urban The scatter diagram of all stations in Beijing, the red is the forecast and

  13. Permeability of fiber reinforcements for liquid composite molding: Sequential multi-scale investigations into numerical flow modeling on the micro- and meso-scale

    NASA Astrophysics Data System (ADS)

    Luchini, Timothy John Franklin

    Composites are complex material mixtures, known to have high amounts of variability, with unique properties at the micro-, meso-, and macro-scales. In the context of advanced textile composite reinforcements, micro-scale refers to aligned fibers and toughening agents in a disordered arrangement; meso-scale is the woven, braided, or stitched fabric geometry (which compacts to various volume fractions); and macro-scale is the component or sub-component being produced for a mechanical application. The Darcy-based permeability is an important parameter for modeling and understanding the flow profile and fill times for liquid composite molding. Permeability of composite materials can vary widely from the micro- to macro-scales. For example, geometric factors like compaction and ply layup affect the component permeability at the meso- and macro-scales. On the micro-scale the permeability will be affected by the packing arrangement of the fibers and fiber volume fraction. On any scale, simplifications to the geometry can be made to treat the fiber reinforcement as a porous media. Permeability has been widely studied in both experimental and analytical frameworks, but less attention has focused on the ability of numerical tools to predict the permeability of reinforced composite materials. This work aims at (1) predicting permeability at various scales of interest and (2) developing a sequential, multi-scale, numerical modeling approach on the micro- and meso-scales. First, a micro-scale modeling approach is developed, including a geometry generation tool and a fluids-based numerical permeability solver. This micro-scale model included all physical fibers and derived the empirical permeability constant directly though numerical simulation. This numerical approach was compared with literature results for perfect packing arrangements, and the results were shown to be comparable with previous work. The numerical simulations described here also extended these previous

  14. Multi-Scale Modelling of Deformation and Fracture in a Biomimetic Apatite-Protein Composite: Molecular-Scale Processes Lead to Resilience at the μm-Scale

    PubMed Central

    Zahn, Dirk; Duchstein, Patrick

    2016-01-01

    Fracture mechanisms of an enamel-like hydroxyapatite-collagen composite model are elaborated by means of molecular and coarse-grained dynamics simulation. Using fully atomistic models, we uncover molecular-scale plastic deformation and fracture processes initiated at the organic-inorganic interface. Furthermore, coarse-grained models are developed to investigate fracture patterns at the μm-scale. At the meso-scale, micro-fractures are shown to reduce local stress and thus prevent material failure after loading beyond the elastic limit. On the basis of our multi-scale simulation approach, we provide a molecular scale rationalization of this phenomenon, which seems key to the resilience of hierarchical biominerals, including teeth and bone. PMID:27300748

  15. Multi-Scale Modelling of Deformation and Fracture in a Biomimetic Apatite-Protein Composite: Molecular-Scale Processes Lead to Resilience at the μm-Scale.

    PubMed

    Zahn, Dirk; Duchstein, Patrick

    2016-01-01

    Fracture mechanisms of an enamel-like hydroxyapatite-collagen composite model are elaborated by means of molecular and coarse-grained dynamics simulation. Using fully atomistic models, we uncover molecular-scale plastic deformation and fracture processes initiated at the organic-inorganic interface. Furthermore, coarse-grained models are developed to investigate fracture patterns at the μm-scale. At the meso-scale, micro-fractures are shown to reduce local stress and thus prevent material failure after loading beyond the elastic limit. On the basis of our multi-scale simulation approach, we provide a molecular scale rationalization of this phenomenon, which seems key to the resilience of hierarchical biominerals, including teeth and bone. PMID:27300748

  16. Impact of air traffic emissions on airport air quality. Multi-scale modeling, test bed and field measurements

    NASA Astrophysics Data System (ADS)

    Ramaroson, R.; Vuillot, F.; Durand, Y.; Courbet, B.; Janin, F.; Copalle, A.; Guin, C.; Paux, E.; Vannier, F.; Talbaut, M.; Weill, M.

    2004-12-01

    Air traffic emissions are playing a significant role in airport air quality. Engine emissions contribute to the ozone and PM formation. There is an emergence of a need to develop advanced numerical tools and airport emission databases for air pollution studies. Field monitoring at airports necessary to support model assessment is still limited in time and space. The French ONERA AIRPUR project has focused on three objectives: emission inventories; dispersion models; field measurements. Results are presented and discussed in this paper. The ground spatial distribution of LTO emissions using realistic aircraft trajectories, aircraft-engine classification by ICAO, fuel flow methodology and diurnal variations of fleet number, is presented and discussed. Exhaust species time evolution is simulated using a chemical-dispersion model. Results show high emissions of NOx during LTO, and a maximum of CO and Hydrocarbons during taxi. Depending on seasons, the NOx lifetime is varying differently; lower concentration is calculated far away from LTO emissions. Longer-lived pollutants such as ozone are formed downstream and require the use of advanced dispersion models. For this reason, two interactive models coupling the micro and the regional scales are developed and used in this work. A 3D CFD model (CEDRE) simulates the flow characteristics around buildings and the dispersion of emissions. CEDRE boundary conditions are provided by the 3D nested dispersion model MEDIUM/MM5, which includes a surface boundary layer chemistry and calculates the concentration of pollutants from the local to the airport vicinities. The CFD results show a tracer accumulation calculated downstream beside terminals, consistent with observations at some mega-airports. Sensibility studies are conducted to highlight the impact of emissions on ozone formation with MEDIUM. Results show that longer-lived species are produced downstream, their concentration depending on NOx, aromatics and VOC released by

  17. Targeting the Biophysical Properties of the Myeloma Initiating Cell Niches: A Pharmaceutical Synergism Analysis Using Multi-Scale Agent-Based Modeling

    PubMed Central

    Su, Jing; Zhang, Le; Zhang, Wen; Choi, Dong Song; Wen, Jianguo; Jiang, Beini; Chang, Chung-Che; Zhou, Xiaobo

    2014-01-01

    Multiple myeloma, the second most common hematological cancer, is currently incurable due to refractory disease relapse and development of multiple drug resistance. We and others recently established the biophysical model that myeloma initiating (stem) cells (MICs) trigger the stiffening of their niches via SDF-1/CXCR4 paracrine; The stiffened niches then promote the colonogenesis of MICs and protect them from drug treatment. In this work we examined in silico the pharmaceutical potential of targeting MIC niche stiffness to facilitate cytotoxic chemotherapies. We first established a multi-scale agent-based model using the Markov Chain Monte Carlo approach to recapitulate the niche stiffness centric, pro-oncogenetic positive feedback loop between MICs and myeloma-associated bone marrow stromal cells (MBMSCs), and investigated the effects of such intercellular chemo-physical communications on myeloma development. Then we used AMD3100 (to interrupt the interactions between MICs and their stroma) and Bortezomib (a recently developed novel therapeutic agent) as representative drugs to examine if the biophysical properties of myeloma niches are drugable. Results showed that our model recaptured the key experimental observation that the MBMSCs were more sensitive to SDF-1 secreted by MICs, and provided stiffer niches for these initiating cells and promoted their proliferation and drug resistance. Drug synergism analysis suggested that AMD3100 treatment undermined the capability of MICs to modulate the bone marrow microenvironment, and thus re-sensitized myeloma to Bortezomib treatments. This work is also the first attempt to virtually visualize in 3D the dynamics of the bone marrow stiffness during myeloma development. In summary, we established a multi-scale model to facilitate the translation of the niche-stiffness centric myeloma model as well as experimental observations to possible clinical applications. We concluded that targeting the biophysical properties of stem

  18. Toward a Multi-Scale Computational Model of Arterial Adaptation in Hypertension: Verification of a Multi-Cell Agent Based Model

    PubMed Central

    Thorne, Bryan C.; Hayenga, Heather N.; Humphrey, Jay D.; Peirce, Shayn M.

    2011-01-01

    Agent-based models (ABMs) represent a novel approach to study and simulate complex mechano chemo-biological responses at the cellular level. Such models have been used to simulate a variety of emergent responses in the vasculature, including angiogenesis and vasculogenesis. Although not used previously to study large vessel adaptations, we submit that ABMs will prove equally useful in such studies when combined with well-established continuum models to form multi-scale models of tissue-level phenomena. In order to couple agent-based and continuum models, however, there is a need to ensure that each model faithfully represents the best data available at the relevant scale and that there is consistency between models under baseline conditions. Toward this end, we describe the development and verification of an ABM of endothelial and smooth muscle cell responses to mechanical stimuli in a large artery. A refined rule-set is proposed based on a broad literature search, a new scoring system for assigning confidence in the rules, and a parameter sensitivity study. To illustrate the utility of these new methods for rule selection, as well as the consistency achieved with continuum-level models, we simulate the behavior of a mouse aorta during homeostasis and in response to both transient and sustained increases in pressure. The simulated responses depend on the altered cellular production of seven key mitogenic, synthetic, and proteolytic biomolecules, which in turn control the turnover of intramural cells and extracellular matrix. These events are responsible for gross changes in vessel wall morphology. This new ABM is shown to be appropriately stable under homeostatic conditions, insensitive to transient elevations in blood pressure, and responsive to increased intramural wall stress in hypertension. PMID:21720536

  19. Complex three dimensional modelling of porous media using high performance computing and multi-scale incompressible approach

    NASA Astrophysics Data System (ADS)

    Martin, R.; Orgogozo, L.; Noiriel, C. N.; Guibert, R.; Golfier, F.; Debenest, G.; Quintard, M.

    2013-05-01

    computed by sending batteries of codes in a mass production procedure. Some constraints can now be provided for poro-elastic imaging at the scale of reservoirs, for CO2 storage monitoring or geophysical exploration. 1. Golfier F. et al., Biofilms in porous media: Development of macroscopic transport equations va volume averaging with closure for local mass equilibrium conditions, Advances in Water Resources, 32, 463-485 (2009). 2. Orgogozo L. et al., Upscaling of transport processes in porous media with biofilms in non-equilibrium conditions, Advances in Water Resources, 33(5), 585-600 (2010). 3. Davit Y. et al., Modeling non-equilibrium mass transport in biologically reactive porous media, Advances in Water Resources, 33, 1075-1093, (2010). 4. Davit Y. et al., Imaging biofilm in porous media using X-ray computed micro-tomography, Journal of Microscopy, 242(1), 15-25 (2010). 5. Noiriel C. et al., Upscaling calcium carbonate precipitation rates from pore to continuum scale, Chemical Geology, 318-319, 60-74 (2012).

  20. Partial lateral forcing experiments reveal how multi-scale processes induce devastating rainfall: a new application of regional modeling

    NASA Astrophysics Data System (ADS)

    Yang, Hongwei; Wang, Bin

    2015-09-01

    The 1998 extremely heavy rainfall events over East Asia are investigated through partial lateral forcing (PLF) experiments with the Weather Research and Forecasting model to determine the impacts of the synoptic (SY), intra-seasonal (IS), and inter-annual (IA) forcing across the lateral boundary on the extreme climate anomalies. The large-scale lateral boundary forcing was derived from an ensemble reanalysis dataset and decomposed into climatological, SY, IS, and IA components. The PLF experiments show that the IS forcing not only triggers the monsoon onset and drives two northward propagation events of the subtropical front but also has dominant contributions to the two heaviest rainfall events over the Yangtze River Basin (YRB) and South China, suggesting the critical role of the intra-seasonal variability in the devastating 1998 floods. Previous studies perceived that the northward propagating IS oscillation from the tropics regulates the extreme heavy rainfall of East Asia summer monsoon in 1998. However, we find that the IS forcing from the mid-latitude plays a more important role than the forcing from the tropics in generating the two extreme rainfall events in 1998. During the first extreme event in June, the IS forcing across the western boundary is the major cause of the northward advance of the subtropical front and the heavy rainfall over the YRB and South China, with the IS forcing across the northern boundary providing the second largest contribution. During the second extreme event (July 15-August 5), the IS forcing from the eastern boundary plays a dominant role in driving the southward retreat and northward advance of the subtropical front, causing another heavy rainfall over the YRB and South China. The western and northern IS forcing also has large contributions to the second extreme event. We have estimated the contributions to the seasonal anomalous rainfall by the three types of forcing. The SY forcing tends to have a moderate effect on the YRB

  1. A multi-scale finite element model for investigation of chondrocyte mechanics in normal and medial meniscectomy human knee joint during walking.

    PubMed

    Tanska, Petri; Mononen, Mika E; Korhonen, Rami K

    2015-06-01

    Mechanical signals experienced by chondrocytes (articular cartilage cells) modulate cell synthesis and cartilage health. Multi-scale modeling can be used to study how forces are transferred from joint surfaces through tissues to chondrocytes. Therefore, estimation of chondrocyte behavior during certain physical activities, such as walking, could provide information about how cells respond to normal and abnormal loading in joints. In this study, a 3D multi-scale model was developed for evaluating chondrocyte and surrounding peri- and extracellular matrix responses during gait loading within healthy and medial meniscectomy knee joints. The knee joint geometry was based on MRI, whereas the input used for gait loading was obtained from the literature. Femoral and tibial cartilages were modeled as fibril-reinforced poroviscoelastic materials, whereas menisci were considered as transversely isotropic. Fluid pressures in the chondrocyte and cartilage tissue increased up to 2MPa (an increase of 30%) in the meniscectomy joint compared to the normal, healthy joint. The elevated level of fluid pressure was observed during the entire stance phase of gait. A medial meniscectomy caused substantially larger (up to 60%) changes in maximum principal strains in the chondrocyte compared to those in the peri- or extracellular matrices. Chondrocyte volume or morphology did not change substantially due to a medial meniscectomy. Current findings suggest that during walking chondrocyte deformations are not substantially altered due to a medial meniscectomy, while abnormal joint loading exposes chondrocytes to elevated levels of fluid pressure and maximum principal strains (compared to strains in the peri- or extracellular matrices). These might contribute to cell viability and the onset of osteoarthritis.

  2. Multi-scale Material Appearance

    NASA Astrophysics Data System (ADS)

    Wu, Hongzhi

    Modeling and rendering the appearance of materials is important for a diverse range of applications of computer graphics - from automobile design to movies and cultural heritage. The appearance of materials varies considerably at different scales, posing significant challenges due to the sheer complexity of the data, as well the need to maintain inter-scale consistency constraints. This thesis presents a series of studies around the modeling, rendering and editing of multi-scale material appearance. To efficiently render material appearance at multiple scales, we develop an object-space precomputed adaptive sampling method, which precomputes a hierarchy of view-independent points that preserve multi-level appearance. To support bi-scale material appearance design, we propose a novel reflectance filtering algorithm, which rapidly computes the large-scale appearance from small-scale details, by exploiting the low-rank structures of Bidirectional Visible Normal Distribution Functions and pre-rotated Bidirectional Reflectance Distribution Functions in the matrix formulation of the rendering algorithm. This approach can guide the physical realization of appearance, as well as the modeling of real-world materials using very sparse measurements. Finally, we present a bi-scale-inspired high-quality general representation for material appearance described by Bidirectional Texture Functions. Our representation is at once compact, easily editable, and amenable to efficient rendering.

  3. Ensemble-based multi-scale assimilation

    NASA Astrophysics Data System (ADS)

    Ravela, S.; Hansen, J.; Hill, C.; Hill, H.; Marshall, J.

    2003-04-01

    We develop ensemble methods for constraining numerical models due to errors induced both by uncertain initial states and model structure. In the present paper, circulation phenomena are physically simulated in a laboratory and sensors are used to extract observations (velocity, temperature, etc.). Ensembles of the MITGCM constructed across variations in state and model-parameterizations are assimilated with observations over sliding multi-scale assimilation windows to regulate the trajectory of the model attractors vis a vis the system attractor. The novel contribution of this work is in bringing together the use of multi-scale assimilations, physical processes of moderate complexity, techniques for extracting flow and providing physically meaningful ways to alter analyses for minimizing model/data misfit.

  4. Multi-scale model of epidemic fade-out: Will local extirpation events inhibit the spread of white-nose syndrome?

    PubMed

    O'Reagan, Suzanne M; Magori, Krisztian; Pulliam, J Tomlin; Zokan, Marcus A; Kaul, RajReni B; Barton, Heather D; Drake, John M

    2015-04-01

    White-nose syndrome (WNS) is an emerging infectious disease that has resulted in severe declines of its hibernating bat hosts in North America. The ongoing epidemic of white-nose syndrome is a multi-scale phenomenon becau.se it causes hibernaculum-level extirpations, while simultaneously spreading over larger spatial scales. We investigate a neglected topic in ecological epidemiology: how local pathogen-driven extirpations impact large-scale pathogen spread. Previous studies have identified risk factors for propagation of WNS over hibernaculum and landscape scales but none of these have tested the hypothesis that separation of spatial scales and disease-induced mortality at the hibernaculum level might slow or halt its spread. To test this hypothesis, we developed a mechanistic multi-scale model parameterized using white-nose syndrome.county and site incidence data that connects hibernaculum-level susceptible-infectious-removed (SIR) epidemiology to the county-scale contagion process. Our key result is that hibernaculum-level extirpations will not inhibit county-scale spread of WNS. We show that over 80% of counties of the contiguous USA are likely to become infected before the current epidemic is over and that geometry of habitat connectivity is such that host refuges are exceedingly rare. The macroscale spatiotemporal infection pattern that emerges from local SIR epidemiological processes falls within a narrow spectrum of possible outcomes, suggesting that recolonization, rescue effects, and multi-host complexities at local scales are not important to forward propagation of WNS at large spatial scales. If effective control measures are not implemented, precipitous declines in bat populations are likely, particularly in cave-dense regions that constitute the main geographic corridors of the USA, a serious concern for bat conservation.

  5. Multi-scale model of epidemic fade-out: Will local extirpation events inhibit the spread of white-nose syndrome?

    PubMed

    O'Reagan, Suzanne M; Magori, Krisztian; Pulliam, J Tomlin; Zokan, Marcus A; Kaul, RajReni B; Barton, Heather D; Drake, John M

    2015-04-01

    White-nose syndrome (WNS) is an emerging infectious disease that has resulted in severe declines of its hibernating bat hosts in North America. The ongoing epidemic of white-nose syndrome is a multi-scale phenomenon becau.se it causes hibernaculum-level extirpations, while simultaneously spreading over larger spatial scales. We investigate a neglected topic in ecological epidemiology: how local pathogen-driven extirpations impact large-scale pathogen spread. Previous studies have identified risk factors for propagation of WNS over hibernaculum and landscape scales but none of these have tested the hypothesis that separation of spatial scales and disease-induced mortality at the hibernaculum level might slow or halt its spread. To test this hypothesis, we developed a mechanistic multi-scale model parameterized using white-nose syndrome.county and site incidence data that connects hibernaculum-level susceptible-infectious-removed (SIR) epidemiology to the county-scale contagion process. Our key result is that hibernaculum-level extirpations will not inhibit county-scale spread of WNS. We show that over 80% of counties of the contiguous USA are likely to become infected before the current epidemic is over and that geometry of habitat connectivity is such that host refuges are exceedingly rare. The macroscale spatiotemporal infection pattern that emerges from local SIR epidemiological processes falls within a narrow spectrum of possible outcomes, suggesting that recolonization, rescue effects, and multi-host complexities at local scales are not important to forward propagation of WNS at large spatial scales. If effective control measures are not implemented, precipitous declines in bat populations are likely, particularly in cave-dense regions that constitute the main geographic corridors of the USA, a serious concern for bat conservation. PMID:26214909

  6. Development of a Patient-Specific Multi-Scale Model to Understand Atherosclerosis and Calcification Locations: Comparison with In vivo Data in an Aortic Dissection.

    PubMed

    Alimohammadi, Mona; Pichardo-Almarza, Cesar; Agu, Obiekezie; Díaz-Zuccarini, Vanessa

    2016-01-01

    Vascular calcification results in stiffening of the aorta and is associated with hypertension and atherosclerosis. Atherogenesis is a complex, multifactorial, and systemic process; the result of a number of factors, each operating simultaneously at several spatial and temporal scales. The ability to predict sites of atherogenesis would be of great use to clinicians in order to improve diagnostic and treatment planning. In this paper, we present a mathematical model as a tool to understand why atherosclerotic plaque and calcifications occur in specific locations. This model is then used to analyze vascular calcification and atherosclerotic areas in an aortic dissection patient using a mechanistic, multi-scale modeling approach, coupling patient-specific, fluid-structure interaction simulations with a model of endothelial mechanotransduction. A number of hemodynamic factors based on state-of-the-art literature are used as inputs to the endothelial permeability model, in order to investigate plaque and calcification distributions, which are compared with clinical imaging data. A significantly improved correlation between elevated hydraulic conductivity or volume flux and the presence of calcification and plaques was achieved by using a shear index comprising both mean and oscillatory shear components (HOLMES) and a non-Newtonian viscosity model as inputs, as compared to widely used hemodynamic indicators. The proposed approach shows promise as a predictive tool. The improvements obtained using the combined biomechanical/biochemical modeling approach highlight the benefits of mechanistic modeling as a powerful tool to understand complex phenomena and provides insight into the relative importance of key hemodynamic parameters. PMID:27445834

  7. Development of a Patient-Specific Multi-Scale Model to Understand Atherosclerosis and Calcification Locations: Comparison with In vivo Data in an Aortic Dissection

    PubMed Central

    Alimohammadi, Mona; Pichardo-Almarza, Cesar; Agu, Obiekezie; Díaz-Zuccarini, Vanessa

    2016-01-01

    Vascular calcification results in stiffening of the aorta and is associated with hypertension and atherosclerosis. Atherogenesis is a complex, multifactorial, and systemic process; the result of a number of factors, each operating simultaneously at several spatial and temporal scales. The ability to predict sites of atherogenesis would be of great use to clinicians in order to improve diagnostic and treatment planning. In this paper, we present a mathematical model as a tool to understand why atherosclerotic plaque and calcifications occur in specific locations. This model is then used to analyze vascular calcification and atherosclerotic areas in an aortic dissection patient using a mechanistic, multi-scale modeling approach, coupling patient-specific, fluid-structure interaction simulations with a model of endothelial mechanotransduction. A number of hemodynamic factors based on state-of-the-art literature are used as inputs to the endothelial permeability model, in order to investigate plaque and calcification distributions, which are compared with clinical imaging data. A significantly improved correlation between elevated hydraulic conductivity or volume flux and the presence of calcification and plaques was achieved by using a shear index comprising both mean and oscillatory shear components (HOLMES) and a non-Newtonian viscosity model as inputs, as compared to widely used hemodynamic indicators. The proposed approach shows promise as a predictive tool. The improvements obtained using the combined biomechanical/biochemical modeling approach highlight the benefits of mechanistic modeling as a powerful tool to understand complex phenomena and provides insight into the relative importance of key hemodynamic parameters. PMID:27445834

  8. Cell mass and cell cycle dynamics of an asynchronous budding yeast population: experimental observations, flow cytometry data analysis, and multi-scale modeling.

    PubMed

    Lencastre Fernandes, Rita; Carlquist, Magnus; Lundin, Luisa; Heins, Anna-Lena; Dutta, Abhishek; Sørensen, Søren J; Jensen, Anker D; Nopens, Ingmar; Lantz, Anna Eliasson; Gernaey, Krist V

    2013-03-01

    Despite traditionally regarded as identical, cells in a microbial cultivation present a distribution of phenotypic traits, forming a heterogeneous cell population. Moreover, the degree of heterogeneity is notably enhanced by changes in micro-environmental conditions. A major development in experimental single-cell studies has taken place in the last decades. It has however not been fully accompanied by similar contributions within data analysis and mathematical modeling. Indeed, literature reporting, for example, quantitative analyses of experimental single-cell observations and validation of model predictions for cell property distributions against experimental data is scarce. This study focuses on the experimental and mathematical description of the dynamics of cell size and cell cycle position distributions, of a population of Saccharomyces cerevisiae, in response to the substrate consumption observed during batch cultivation. The good agreement between the proposed multi-scale model (a population balance model [PBM] coupled to an unstructured model) and experimental data (both the overall physiology and cell size and cell cycle distributions) indicates that a mechanistic model is a suitable tool for describing the microbial population dynamics in a bioreactor. This study therefore contributes towards the understanding of the development of heterogeneous populations during microbial cultivations. More generally, it consists of a step towards a paradigm change in the study and description of cell cultivations, where average cell behaviors observed experimentally now are interpreted as a potential joint result of various co-existing single-cell behaviors, rather than a unique response common to all cells in the cultivation.

  9. Scale separation for multi-scale modeling of free-surface and two-phase flows with the conservative sharp interface method

    SciTech Connect

    Han, L.H. Hu, X.Y. Adams, N.A.

    2015-01-01

    In this paper we present a scale separation approach for multi-scale modeling of free-surface and two-phase flows with complex interface evolution. By performing a stimulus-response operation on the level-set function representing the interface, separation of resolvable and non-resolvable interface scales is achieved efficiently. Uniform positive and negative shifts of the level-set function are used to determine non-resolvable interface structures. Non-resolved interface structures are separated from the resolved ones and can be treated by a mixing model or a Lagrangian-particle model in order to preserve mass. Resolved interface structures are treated by the conservative sharp-interface model. Since the proposed scale separation approach does not rely on topological information, unlike in previous work, it can be implemented in a straightforward fashion into a given level set based interface model. A number of two- and three-dimensional numerical tests demonstrate that the proposed method is able to cope with complex interface variations accurately and significantly increases robustness against underresolved interface structures.

  10. The motion of Hurricane-like vortices determined by multi-scale interactions between the mesoscale vortex flow and its large-scale environment: a theoretical model

    NASA Astrophysics Data System (ADS)

    Päschke, E.; Klein, R.

    2009-04-01

    Research in recent years have shown that multi-scale processes play a nontrivial role in tropical cyclone development, motion and structure. For example, important multi-scale processes that determine these vortex features arise from interactions between the vortex flow itself, its environmental flow, the Coriolis force due to the earth's rotation and diabatic effects as a consequence of moisture conversion processes occuring in convective cloud systems. Concerning the vortex motion it is well known that the large-scale environmental flow acts as a steering flow. Beta-gyres arising from interactions between the vortex flow and the earth's vorticity field contribute to a deviation of the storm track from the steering flow. Interactions between mesoscale vortices and small scale convective systems are assumed to be responsible for the tendency of tropical cyclones to meander about a mean path, which can be seen in long-range observations based on modern satellite techniques. The structure and intensity changes of tropical cyclones strongly depend from both diabatic effects and the environmental flow. For instance, it is observed that an unfavourable condition for a hurricane to develop or survive is given by a strong vertical shear in the environmental flow. One common explanation for this is that the dispersion of heat as a consequence of disruption of organized pattern of convection by strong winds aloft is responsible for a weakening or limiting of the development of mature storms. We present a threedimensional model to describe the motion and structure of Hurricane strength H1/H2 vortices. From a theoretical point of view this model gives deeper insight how the mesoscale structure of the vortex itself affects the synoptic scale vortex motion and vice versa, while taking the influence of a vertically sheared environmental flow and diabatic effects due to moisture conversion processes into account. The derivation of the model equations is based on matched

  11. Multi-scale Modeling Study of poly(3-hexylthiophene) and [6 6]-phenyl-C61-butyric acid methyl ester Towards Organic Photovoltaic Cell Application

    NASA Astrophysics Data System (ADS)

    Yoo, Hanjong; Kim, Ki Chul; Jang, Seung Soon

    2015-03-01

    To date, organic photovoltaic cells have gained attention due to their promising potential in the industry. Its efficiency needs to be improved through constructing better morphologies. There are three morphological quantities that affect the efficiency. The domain size of the electron donor phase has to be small and the interface-to-volume ratio of the blend must be large. The percolation ratio has to be high. To investigate the morphological properties of the active layer systems, the state-of-the-art multi-scale modeling is employed. In this study, P3HT and PCBM blends have used as our active layer candidates. We have developed our own force field parameters to accurately describe potential energy surfaces in the layer systems. Subsequently, coarse-grained force field for P3HT and PCBM have been developed based on the improved atomistic force field parameters in order to simulate larger systems. The results from coarse-grained models are validated through the comparison with those from the full atomistic models. Using the molecular dynamics simulations, the newly developed coarse-grained models will be further used to study how the crystallinity of P3HT affects the morphological properties in the active layers.

  12. Multi-Scale Infrastructure Assessment

    EPA Science Inventory

    The U.S. Environmental Protection Agency’s (EPA) multi-scale infrastructure assessment project supports both water resource adaptation to climate change and the rehabilitation of the nation’s aging water infrastructure by providing tools, scientific data and information to progra...

  13. Modeling the Distribution of African Savanna Elephants in Kruger National Park: AN Application of Multi-Scale GLOBELAND30 Data

    NASA Astrophysics Data System (ADS)

    Xu, W.; Hays, B.; Fayrer-Hosken, R.; Presotto, A.

    2016-06-01

    The ability of remote sensing to represent ecologically relevant features at multiple spatial scales makes it a powerful tool for studying wildlife distributions. Species of varying sizes perceive and interact with their environment at differing scales; therefore, it is important to consider the role of spatial resolution of remotely sensed data in the creation of distribution models. The release of the Globeland30 land cover classification in 2014, with its 30 m resolution, presents the opportunity to do precisely that. We created a series of Maximum Entropy distribution models for African savanna elephants (Loxodonta africana) using Globeland30 data analyzed at varying resolutions. We compared these with similarly re-sampled models created from the European Space Agency's Global Land Cover Map (Globcover). These data, in combination with GIS layers of topography and distance to roads, human activity, and water, as well as elephant GPS collar data, were used with MaxEnt software to produce the final distribution models. The AUC (Area Under the Curve) scores indicated that the models created from 600 m data performed better than other spatial resolutions and that the Globeland30 models generally performed better than the Globcover models. Additionally, elevation and distance to rivers seemed to be the most important variables in our models. Our results demonstrate that Globeland30 is a valid alternative to the well-established Globcover for creating wildlife distribution models. It may even be superior for applications which require higher spatial resolution and less nuanced classifications.

  14. Clouds, weather, climate, and modeling for K-12 and public audiences from the Center for Multi-scale Modeling of Atmospheric Processes

    NASA Astrophysics Data System (ADS)

    Foster, S. Q.; Johnson, R. M.; Randall, D. A.; Denning, A.; Russell, R. M.; Gardiner, L. S.; Hatheway, B.; Jones, B.; Burt, M. A.; Genyuk, J.

    2010-12-01

    The need for improving the representation of cloud processes in climate models has been one of the most important limitations of the reliability of climate-change simulations. Now in its fifth year, the National Science Foundation-funded Center for Multi-scale Modeling of Atmospheric Processes (CMMAP) at Colorado State University (CSU) is addressing this problem through a revolutionary new approach to representing cloud processes on their native scales, including the cloud-scale interaction processes that are active in cloud systems. CMMAP has set ambitious education and human-resource goals to share basic information about the atmosphere, clouds, weather, climate, and modeling with diverse K-12 and public audiences. This is accomplished through collaborations in resource development and dissemination between CMMAP scientists, CSU’s Little Shop of Physics (LSOP) program, and the Windows to the Universe (W2U) program at University Corporation for Atmospheric Research (UCAR). Little Shop of Physics develops new hands on science activities demonstrating basic science concepts fundamental to understanding atmospheric characteristics, weather, and climate. Videos capture demonstrations of children completing these activities which are broadcast to school districts and public television programs. CMMAP and LSOP educators and scientists partner in teaching a summer professional development workshops for teachers at CSU with a semester's worth of college-level content on the basic physics of the atmosphere, weather, climate, climate modeling, and climate change, as well as dozens of LSOP inquiry-based activities suitable for use in classrooms. The W2U project complements these efforts by developing and broadly disseminating new CMMAP-related online content pages, animations, interactives, image galleries, scientists’ biographies, and LSOP videos to K-12 and public audiences. Reaching nearly 20 million users annually, W2U is highly valued as a curriculum enhancement

  15. Modeling ozone and aerosol formation and transport in the pacific northwest with the community Multi-Scale Air Quality (CMAQ) modeling system.

    PubMed

    O'Neill, Susan M; Lamb, Brian K; Chen, Jack; Claiborn, Candis; Finn, Dennis; Otterson, Sally; Figueroa, Cristiana; Bowman, Clint; Boyer, Mike; Wilson, Rob; Arnold, Jeff; Aalbers, Steven; Stocum, Jeffrey; Swab, Christopher; Stoll, Matt; Dubois, Mike; Anderson, Mary

    2006-02-15

    The Community Multi-Scale Air Quality (CMAQ) modeling system was used to investigate ozone and aerosol concentrations in the Pacific Northwest (PNW) during hot summertime conditions during July 1-15, 1996. Two emission inventories (El) were developed: emissions for the first El were based upon the National Emission Trend 1996 (NET96) database and the BEIS2 biogenic emission model, and emissions for the second El were developed through a "bottom up" approach that included biogenic emissions obtained from the GLOBEIS model. The two simulations showed that elevated PM2.5 concentrations occurred near and downwind of the Interstate-5 corridor along the foothills of the Cascade Mountains and in forested areas of central Idaho. The relative contributions of organic and inorganic aerosols varied by region, but generally organic aerosols constituted the largest fraction of PM2.5. In wilderness areas near the 1-5 corridor, organic carbon from anthropogenic sources contributed approximately 50% of the total organic carbon with the remainder from biogenic precursors, while in wilderness areas in Idaho, biogenic organic carbon accounted for 80% of the total organic aerosol. Regional analysis of the secondary organic aerosol formation in the Columbia River Gorge, Central Idaho, and the Olympics/Puget Sound showed that the production rate of secondary organic carbon depends on local terpene concentrations and the local oxidizing capacity of the atmosphere, which was strongly influenced by anthropogenic emissions. Comparison with observations from 12 IMPROVE sites and 21 ozone monitoring sites showed that results from the two El simulations generally bracketed the average observed PM parameters and that errors calculated for the model results were within acceptable bounds. Analysis across all statistical parameters indicated that the NW-AIRQUEST El solution performed better at predicting PM2.5, PM1, and beta(ext) even though organic carbon PM was over-predicted, and the NET96 El

  16. Modeling ozone and aerosol formation and transport in the pacific northwest with the community Multi-Scale Air Quality (CMAQ) modeling system.

    PubMed

    O'Neill, Susan M; Lamb, Brian K; Chen, Jack; Claiborn, Candis; Finn, Dennis; Otterson, Sally; Figueroa, Cristiana; Bowman, Clint; Boyer, Mike; Wilson, Rob; Arnold, Jeff; Aalbers, Steven; Stocum, Jeffrey; Swab, Christopher; Stoll, Matt; Dubois, Mike; Anderson, Mary

    2006-02-15

    The Community Multi-Scale Air Quality (CMAQ) modeling system was used to investigate ozone and aerosol concentrations in the Pacific Northwest (PNW) during hot summertime conditions during July 1-15, 1996. Two emission inventories (El) were developed: emissions for the first El were based upon the National Emission Trend 1996 (NET96) database and the BEIS2 biogenic emission model, and emissions for the second El were developed through a "bottom up" approach that included biogenic emissions obtained from the GLOBEIS model. The two simulations showed that elevated PM2.5 concentrations occurred near and downwind of the Interstate-5 corridor along the foothills of the Cascade Mountains and in forested areas of central Idaho. The relative contributions of organic and inorganic aerosols varied by region, but generally organic aerosols constituted the largest fraction of PM2.5. In wilderness areas near the 1-5 corridor, organic carbon from anthropogenic sources contributed approximately 50% of the total organic carbon with the remainder from biogenic precursors, while in wilderness areas in Idaho, biogenic organic carbon accounted for 80% of the total organic aerosol. Regional analysis of the secondary organic aerosol formation in the Columbia River Gorge, Central Idaho, and the Olympics/Puget Sound showed that the production rate of secondary organic carbon depends on local terpene concentrations and the local oxidizing capacity of the atmosphere, which was strongly influenced by anthropogenic emissions. Comparison with observations from 12 IMPROVE sites and 21 ozone monitoring sites showed that results from the two El simulations generally bracketed the average observed PM parameters and that errors calculated for the model results were within acceptable bounds. Analysis across all statistical parameters indicated that the NW-AIRQUEST El solution performed better at predicting PM2.5, PM1, and beta(ext) even though organic carbon PM was over-predicted, and the NET96 El

  17. Mechanical integrity of a carbon nanotube/copper-based through-silicon via for 3D integrated circuits: a multi-scale modeling approach

    NASA Astrophysics Data System (ADS)

    Awad, Ibrahim; Ladani, Leila

    2015-12-01

    Carbon nanotube (CNT)/copper (Cu) composite material is proposed to replace Cu-based through-silicon vias (TSVs) in micro-electronic packages. The proposed material is believed to offer extraordinary mechanical and electrical properties and the presence of CNTs in Cu is believed to overcome issues associated with miniaturization of Cu interconnects, such as electromigration. This study introduces a multi-scale modeling of the proposed TSV in order to evaluate its mechanical integrity under mechanical and thermo-mechanical loading conditions. Molecular dynamics (MD) simulation was used to determine CNT/Cu interface adhesion properties. A cohesive zone model (CZM) was found to be most appropriate to model the interface adhesion, and CZM parameters at the nanoscale were determined using MD simulation. CZM parameters were then used in the finite element analysis in order to understand the mechanical and thermo-mechanical behavior of composite TSV at micro-scale. From the results, CNT/Cu separation does not take place prior to plastic deformation of Cu in bending, and separation does not take place when standard thermal cycling is applied. Further investigation is recommended in order to alleviate the increased plastic deformation in Cu at the CNT/Cu interface in both loading conditions.

  18. Hierarchical Multi-Scale Framework for Materials Modeling: Equation of State Implementation and Application to a Taylor Anvil Impact Test of RDX

    NASA Astrophysics Data System (ADS)

    Barnes, Brian; Spear, Carrie; Leiter, Ken; Becker, Richard; Knap, Jaroslaw; Lisal, Martin; Brennan, John

    2015-06-01

    In order to progress towards a materials-by-design capability, we present work on a challenge in continuum-scale modeling: the direct incorporation of complex physical processes in the constitutive evaluation. In this work, we use an adaptive hierarchical multi-scale (HMS) framework running in parallel on a heterogeneous computational environment to couple a fine-scale, particle-based model computing the equation of state (EOS) to the constitutive response in a finite-element multi-physics simulation. The EOS is obtained from high-fidelity materials simulations performed via dissipative particle dynamics methods. This HMS framework is progress towards an innovation infrastructure that will be of great utility for systems in which essential aspects of the material response are too complex to capture by closed form material models. The design, implementation, and performance of the HMS framework are discussed. Also presented is a proof-of-concept Taylor anvil impact test of non-reacting 1,3,5-trinitroperhydro-1,3,5-triazine (RDX).

  19. Multi-scale biomarker evaluation of the toxicity of a commercial azo dye (Disperse Red 1) in an animal model, the freshwater cnidarian Hydra attenuata.

    PubMed

    de Jong, Laetitia; Pech, Nicolas; de Aragão Umbuzeiro, Gisela; Moreau, Xavier

    2016-06-01

    Acute (24 h, 48 h, 72 h) and chronic (7 days) tests have been performed to evaluate the effects of the commercial azo dye Disperse Red 1 (DR1) using various biomarkers in the freshwater invertebrate Hydra attenuata. Morphological changes have been selected to calculate ecotoxicological thresholds for sublethal and lethal DR1 concentrations. A multinomial logistic model showed that the probability of each morphological stage occurrence was function of concentration, time and interaction between both. Results of oxidative balance parameter measurements (72 h and 7 days) suggest that polyps set up defense mechanisms to limit lipid peroxidation caused by DR1. DR1 exposure at hormetic concentrations induces increase of asexual reproductive rates. This result suggests (1) an impact on the fitness-related phenotypical traits and (2) trade-offs between reproduction and maintenance to allow the population to survive harsher conditions. Changes in serotonin immuno-labeling in polyps showing alterations in feeding behavior suggest that chronic DR1 exposure impaired neuronal processes related to ingesting behavior in H. attenuata. This ecotoxicity study sheds light on the possible serotonin function in Hydra model and reports for the first time that serotonin could play a significant role in feeding behavior. This study used a multi-scale biomarker approach investigating biochemical, morphological, reproductive and behavioral endpoints in Hydra attenuata. This organism is proposed for a pertinent animal model to assess ecotoxicological impact of pollutant mixtures in freshwater environment. PMID:27019466

  20. Mechanical integrity of a carbon nanotube/copper-based through-silicon via for 3D integrated circuits: a multi-scale modeling approach.

    PubMed

    Awad, Ibrahim; Ladani, Leila

    2015-12-01

    Carbon nanotube (CNT)/copper (Cu) composite material is proposed to replace Cu-based through-silicon vias (TSVs) in micro-electronic packages. The proposed material is believed to offer extraordinary mechanical and electrical properties and the presence of CNTs in Cu is believed to overcome issues associated with miniaturization of Cu interconnects, such as electromigration. This study introduces a multi-scale modeling of the proposed TSV in order to evaluate its mechanical integrity under mechanical and thermo-mechanical loading conditions. Molecular dynamics (MD) simulation was used to determine CNT/Cu interface adhesion properties. A cohesive zone model (CZM) was found to be most appropriate to model the interface adhesion, and CZM parameters at the nanoscale were determined using MD simulation. CZM parameters were then used in the finite element analysis in order to understand the mechanical and thermo-mechanical behavior of composite TSV at micro-scale. From the results, CNT/Cu separation does not take place prior to plastic deformation of Cu in bending, and separation does not take place when standard thermal cycling is applied. Further investigation is recommended in order to alleviate the increased plastic deformation in Cu at the CNT/Cu interface in both loading conditions.

  1. Mechanical integrity of a carbon nanotube/copper-based through-silicon via for 3D integrated circuits: a multi-scale modeling approach.

    PubMed

    Awad, Ibrahim; Ladani, Leila

    2015-12-01

    Carbon nanotube (CNT)/copper (Cu) composite material is proposed to replace Cu-based through-silicon vias (TSVs) in micro-electronic packages. The proposed material is believed to offer extraordinary mechanical and electrical properties and the presence of CNTs in Cu is believed to overcome issues associated with miniaturization of Cu interconnects, such as electromigration. This study introduces a multi-scale modeling of the proposed TSV in order to evaluate its mechanical integrity under mechanical and thermo-mechanical loading conditions. Molecular dynamics (MD) simulation was used to determine CNT/Cu interface adhesion properties. A cohesive zone model (CZM) was found to be most appropriate to model the interface adhesion, and CZM parameters at the nanoscale were determined using MD simulation. CZM parameters were then used in the finite element analysis in order to understand the mechanical and thermo-mechanical behavior of composite TSV at micro-scale. From the results, CNT/Cu separation does not take place prior to plastic deformation of Cu in bending, and separation does not take place when standard thermal cycling is applied. Further investigation is recommended in order to alleviate the increased plastic deformation in Cu at the CNT/Cu interface in both loading conditions. PMID:26559788

  2. Mathematical multi-scale model of the cardiovascular system including mitral valve dynamics. Application to ischemic mitral insufficiency

    PubMed Central

    2011-01-01

    Background Valve dysfunction is a common cardiovascular pathology. Despite significant clinical research, there is little formal study of how valve dysfunction affects overall circulatory dynamics. Validated models would offer the ability to better understand these dynamics and thus optimize diagnosis, as well as surgical and other interventions. Methods A cardiovascular and circulatory system (CVS) model has already been validated in silico, and in several animal model studies. It accounts for valve dynamics using Heaviside functions to simulate a physiologically accurate "open on pressure, close on flow" law. However, it does not consider real-time valve opening dynamics and therefore does not fully capture valve dysfunction, particularly where the dysfunction involves partial closure. This research describes an updated version of this previous closed-loop CVS model that includes the progressive opening of the mitral valve, and is defined over the full cardiac cycle. Results Simulations of the cardiovascular system with healthy mitral valve are performed, and, the global hemodynamic behaviour is studied compared with previously validated results. The error between resulting pressure-volume (PV) loops of already validated CVS model and the new CVS model that includes the progressive opening of the mitral valve is assessed and remains within typical measurement error and variability. Simulations of ischemic mitral insufficiency are also performed. Pressure-Volume loops, transmitral flow evolution and mitral valve aperture area evolution follow reported measurements in shape, amplitude and trends. Conclusions The resulting cardiovascular system model including mitral valve dynamics provides a foundation for clinical validation and the study of valvular dysfunction in vivo. The overall models and results could readily be generalised to other cardiac valves. PMID:21942971

  3. Multi-scale defect interactions in high-rate brittle material failure. Part I: Model formulation and application to ALON

    NASA Astrophysics Data System (ADS)

    Tonge, Andrew L.; Ramesh, K. T.

    2016-01-01

    Within this two part series we develop a new material model for ceramic protection materials to provide an interface between microstructural parameters and bulk continuum behavior to provide guidance for materials design activities. Part I of this series focuses on the model formulation that captures the strength variability and strain rate sensitivity of brittle materials and presents a statistical approach to assigning the local flaw distribution within a specimen. The material model incorporates a Mie-Grüneisen equation of state, micromechanics based damage growth, granular flow and dilatation of the highly damaged material, and pore compaction for the porosity introduced by granular flow. To provide initial qualitative validation and illustrate the usefulness of the model, we use the model to investigate Edge on Impact experiments (Strassburger, 2004) on Aluminum Oxynitride (AlON), and discuss the interactions of multiple mechanisms during such an impact event. Part II of this series is focused on additional qualitative validation and using the model to suggest material design directions for boron carbide.

  4. Multi-Scale Validation of a Nanodiamond Drug Delivery System and Multi-Scale Engineering Education

    ERIC Educational Resources Information Center

    Schwalbe, Michelle Kristin

    2010-01-01

    This dissertation has two primary concerns: (i) evaluating the uncertainty and prediction capabilities of a nanodiamond drug delivery model using Bayesian calibration and bias correction, and (ii) determining conceptual difficulties of multi-scale analysis from an engineering education perspective. A Bayesian uncertainty quantification scheme…

  5. Multi-scale spatio-temporal modeling: lifelines of microorganisms in bioreactors and tracking molecules in cells.

    PubMed

    Lapin, Alexei; Klann, Michael; Reuss, Matthias

    2010-01-01

    Agent-based models are rigorous tools for simulating the interactions of individual entities, such as organisms or molecules within cells and assessing their effects on the dynamic behavior of the system as a whole. In context with bioprocess and biosystems engineering there are several interesting and important applications. This contribution aims at introducing this strategy with the aid of two examples characterized by striking distinctions in the scale of the individual entities and the mode of their interactions. In the first example a structured-segregated model is applied to travel along the lifelines of single cells in the environment of a three-dimensional turbulent field of a stirred bioreactor. The modeling approach is based on an Euler-Lagrange formulation of the system. The strategy permits one to account for the heterogeneity present in real reactors in both the fluid and cellular phases, respectively. The individual response of the cells to local variations in the extracellular concentrations is pictured by a dynamically structured model of the key reactions of the central metabolism. The approach permits analysis of the lifelines of individual cells in space and time.The second application of the individual modeling approach deals with dynamic modeling of signal transduction pathways in individual cells. Usually signal transduction networks are portrayed as being wired together in a spatially defined manner. Living circuitry, however, is placed in highly malleable internal architecture. Creating a homogenous bag of molecules, a well-mixed system, the dynamic behavior of which is modeled with a set of ordinary differential equations is normally not valid. The dynamics of the MAP kinase and a steroid hormone pathway serve as examples to illustrate how single molecule tracking can be linked with the stochasticity of biochemical reactions, where diffusion and reaction occur in a probabilistic manner. The problem of hindered diffusion caused by

  6. A multi-scale distribution model for non-equilibrium populations suggests resource limitation in an endangered rodent.

    PubMed

    Bean, William T; Stafford, Robert; Butterfield, H Scott; Brashares, Justin S

    2014-01-01

    Species distributions are known to be limited by biotic and abiotic factors at multiple temporal and spatial scales. Species distribution models, however, frequently assume a population at equilibrium in both time and space. Studies of habitat selection have repeatedly shown the difficulty of estimating resource selection if the scale or extent of analysis is incorrect. Here, we present a multi-step approach to estimate the realized and potential distribution of the endangered giant kangaroo rat. First, we estimate the potential distribution by modeling suitability at a range-wide scale using static bioclimatic variables. We then examine annual changes in extent at a population-level. We define "available" habitat based on the total suitable potential distribution at the range-wide scale. Then, within the available habitat, model changes in population extent driven by multiple measures of resource availability. By modeling distributions for a population with robust estimates of population extent through time, and ecologically relevant predictor variables, we improved the predictive ability of SDMs, as well as revealed an unanticipated relationship between population extent and precipitation at multiple scales. At a range-wide scale, the best model indicated the giant kangaroo rat was limited to areas that received little to no precipitation in the summer months. In contrast, the best model for shorter time scales showed a positive relation with resource abundance, driven by precipitation, in the current and previous year. These results suggest that the distribution of the giant kangaroo rat was limited to the wettest parts of the drier areas within the study region. This multi-step approach reinforces the differing relationship species may have with environmental variables at different scales, provides a novel method for defining "available" habitat in habitat selection studies, and suggests a way to create distribution models at spatial and temporal scales

  7. A Multi-Scale Distribution Model for Non-Equilibrium Populations Suggests Resource Limitation in an Endangered Rodent

    PubMed Central

    Bean, William T.; Stafford, Robert; Butterfield, H. Scott; Brashares, Justin S.

    2014-01-01

    Species distributions are known to be limited by biotic and abiotic factors at multiple temporal and spatial scales. Species distribution models, however, frequently assume a population at equilibrium in both time and space. Studies of habitat selection have repeatedly shown the difficulty of estimating resource selection if the scale or extent of analysis is incorrect. Here, we present a multi-step approach to estimate the realized and potential distribution of the endangered giant kangaroo rat. First, we estimate the potential distribution by modeling suitability at a range-wide scale using static bioclimatic variables. We then examine annual changes in extent at a population-level. We define “available” habitat based on the total suitable potential distribution at the range-wide scale. Then, within the available habitat, model changes in population extent driven by multiple measures of resource availability. By modeling distributions for a population with robust estimates of population extent through time, and ecologically relevant predictor variables, we improved the predictive ability of SDMs, as well as revealed an unanticipated relationship between population extent and precipitation at multiple scales. At a range-wide scale, the best model indicated the giant kangaroo rat was limited to areas that received little to no precipitation in the summer months. In contrast, the best model for shorter time scales showed a positive relation with resource abundance, driven by precipitation, in the current and previous year. These results suggest that the distribution of the giant kangaroo rat was limited to the wettest parts of the drier areas within the study region. This multi-step approach reinforces the differing relationship species may have with environmental variables at different scales, provides a novel method for defining “available” habitat in habitat selection studies, and suggests a way to create distribution models at spatial and temporal scales

  8. Population Estimation Using a 3D City Model: A Multi-Scale Country-Wide Study in the Netherlands

    PubMed Central

    Arroyo Ohori, Ken; Ledoux, Hugo; Peters, Ravi; Stoter, Jantien

    2016-01-01

    The remote estimation of a region’s population has for decades been a key application of geographic information science in demography. Most studies have used 2D data (maps, satellite imagery) to estimate population avoiding field surveys and questionnaires. As the availability of semantic 3D city models is constantly increasing, we investigate to what extent they can be used for the same purpose. Based on the assumption that housing space is a proxy for the number of its residents, we use two methods to estimate the population with 3D city models in two directions: (1) disaggregation (areal interpolation) to estimate the population of small administrative entities (e.g. neighbourhoods) from that of larger ones (e.g. municipalities); and (2) a statistical modelling approach to estimate the population of large entities from a sample composed of their smaller ones (e.g. one acquired by a government register). Starting from a complete Dutch census dataset at the neighbourhood level and a 3D model of all 9.9 million buildings in the Netherlands, we compare the population estimates obtained by both methods with the actual population as reported in the census, and use it to evaluate the quality that can be achieved by estimations at different administrative levels. We also analyse how the volume-based estimation enabled by 3D city models fares in comparison to 2D methods using building footprints and floor areas, as well as how it is affected by different levels of semantic detail in a 3D city model. We conclude that 3D city models are useful for estimations of large areas (e.g. for a country), and that the 3D approach has clear advantages over the 2D approach. PMID:27254151

  9. Population Estimation Using a 3D City Model: A Multi-Scale Country-Wide Study in the Netherlands.

    PubMed

    Biljecki, Filip; Arroyo Ohori, Ken; Ledoux, Hugo; Peters, Ravi; Stoter, Jantien

    2016-01-01

    The remote estimation of a region's population has for decades been a key application of geographic information science in demography. Most studies have used 2D data (maps, satellite imagery) to estimate population avoiding field surveys and questionnaires. As the availability of semantic 3D city models is constantly increasing, we investigate to what extent they can be used for the same purpose. Based on the assumption that housing space is a proxy for the number of its residents, we use two methods to estimate the population with 3D city models in two directions: (1) disaggregation (areal interpolation) to estimate the population of small administrative entities (e.g. neighbourhoods) from that of larger ones (e.g. municipalities); and (2) a statistical modelling approach to estimate the population of large entities from a sample composed of their smaller ones (e.g. one acquired by a government register). Starting from a complete Dutch census dataset at the neighbourhood level and a 3D model of all 9.9 million buildings in the Netherlands, we compare the population estimates obtained by both methods with the actual population as reported in the census, and use it to evaluate the quality that can be achieved by estimations at different administrative levels. We also analyse how the volume-based estimation enabled by 3D city models fares in comparison to 2D methods using building footprints and floor areas, as well as how it is affected by different levels of semantic detail in a 3D city model. We conclude that 3D city models are useful for estimations of large areas (e.g. for a country), and that the 3D approach has clear advantages over the 2D approach. PMID:27254151

  10. Finite element simulation and analytical modeling of 3D multi scale diffusion in nanocomposites with permeable stacks

    NASA Astrophysics Data System (ADS)

    Greco, A.; Maffezzoli, A.

    2016-01-01

    This work is aimed to study the mass transport in 3D nanocomposites, characterized by the presence of permeable lamellar stacks, by means of finite element (FE) analysis. To this purpose, a geometric model was developed, based on a random distribution of non-interpenetrating stacks, each one made of regularly spaced platelets, which are considered representative of an intercalated nanocomposite. The morphological features of the stacks are the number of lamellae and the thickness of lamellar galleries, which determine the thickness, and therefore the aspect ratio. FE simulation results showed the relevance of diffusion within stack, and therefore the unsuitableness of the assumption of stack impermeability. The diffusion behavior of nanocomposites made of permeable stacks was modeled by considering the probability of collision of diffusing particles on the stack surface. For a random orientation of stacks, the developed analytical model showed an excellent agreement with the FE simulation results. It was shown that other analytical models found in literature are not able to capture the dependence of diffusivity on the morphology of intercalated nanocomposites. The developed analytical model allowed estimating the error arising from the assumption of impermeable stacks in the estimation of nanofiller aspect ratio from experimental diffusivity data.

  11. True-false lumen segmentation of aortic dissection using multi-scale wavelet analysis and generative-discriminative model matching

    NASA Astrophysics Data System (ADS)

    Lee, Noah; Tek, Huseyin; Laine, Andrew F.

    2008-03-01

    Computer aided diagnosis in the medical image domain requires sophisticated probabilistic models to formulate quantitative behavior in image space. In the diagnostic process detailed knowledge of model performance with respect to accuracy, variability, and uncertainty is crucial. This challenge has lead to the fusion of two successful learning schools namely generative and discriminative learning. In this paper, we propose a generative-discriminative learning approach to predict object boundaries in medical image datasets. In our approach, we perform probabilistic model matching of both modeling domains to fuse into the prediction step appearance and structural information of the object of interest while exploiting the strength of both learning paradigms. In particular, we apply our method to the task of true-false lumen segmentation of aortic dissections an acute disease that requires automated quantification for assisted medical diagnosis. We report empirical results for true-false lumen discrimination of aortic dissection segmentation showing superior behavior of the hybrid generative-discriminative approach over their non hybrid generative counterpart.

  12. Multi-Scale Spatio-Temporal Modeling: Lifelines of Microorganisms in Bioreactors and Tracking Molecules in Cells

    NASA Astrophysics Data System (ADS)

    Lapin, Alexei; Klann, Michael; Reuss, Matthias

    Agent-based models are rigorous tools for simulating the interactions of individual entities, such as organisms or molecules within cells and assessing their effects on the dynamic behavior of the system as a whole. In context with bioprocess and biosystems engineering there are several interesting and important applications. This contribution aims at introducing this strategy with the aid of two examples characterized by striking distinctions in the scale of the individual entities and the mode of their interactions. In the first example a structured-segregated model is applied to travel along the lifelines of single cells in the environment of a three-dimensional turbulent field of a stirred bioreactor. The modeling approach is based on an Euler-Lagrange formulation of the system. The strategy permits one to account for the heterogeneity present in real reactors in both the fluid and cellular phases, respectively. The individual response of the cells to local variations in the extracellular concentrations is pictured by a dynamically structured model of the key reactions of the central metabolism. The approach permits analysis of the lifelines of individual cells in space and time.

  13. Pro-arrhythmogenic effects of CACNA1C G1911R mutation in human ventricular tachycardia: insights from cardiac multi-scale models.

    PubMed

    Bai, Jieyun; Wang, Kuanquan; Li, Qince; Yuan, Yongfeng; Zhang, Henggui

    2016-01-01

    Mutations in the CACNA1C gene are associated with ventricular tachycardia (VT). Although the CACNA1C mutations were well identified in patients with cardiac arrhythmias, mechanisms by which cardiac arrhythmias are generated in such genetic mutation conditions remain unclear. In this study, we identified a novel mechanism of VT resulted from enhanced repolarization dispersion which is a key factor for arrhythmias in the CACNA1C G1911R mutation using multi-scale computational models of the human ventricle. The increased calcium influx in the mutation prolonged action potential duration (APD), produced steepened action potential duration restitution (APDR) curves as well as augmented membrane potential differences among different cell types during repolarization, increasing transmural dispersion of repolarization (DOR) and the spatial and temporal heterogeneity of cardiac electrical activities. Consequentially, the vulnerability to unidirectional conduction block in response to a premature stimulus increased at tissue level in the G1911R mutation. The increased functional repolarization dispersion anchored reentrant excitation waves in tissue and organ models, facilitating the initiation and maintenance of VT due to less meandering rotor tip. Thus, the increased repolarization dispersion caused by the G1911R mutation is a primary factor that may primarily contribute to the genesis of cardiac arrhythmias in Timothy Syndrome. PMID:27502440

  14. Detection of multi-scale secondary flow structures using anisotropic 2D Ricker wavelets in a bent tube model for curved arteries

    NASA Astrophysics Data System (ADS)

    Plesniak, Daniel H.; Bulusu, Kartik V.; Plesniak, Michael W.

    2012-11-01

    Interpretation of complex flow patterns observed in this study of a model curved artery required characterization of multiple, low-circulation secondary flow structures that were observed during the late systolic deceleration and diastolic phases under physiological inflow conditions. Phase-locked, planar vorticity PIV data were acquired at various cross-sectional locations of the 180-degree bent tube model. High circulation, deformed Dean- and Lyne-type vortices were observed during early stages of deceleration, while several smaller scale, highly deformed, low-circulation vortical patterns appeared in the core and near-wall regions during late systolic deceleration and diastolic phases. Due to the multiplicity of vortical scales and shapes, anisotropic 2D Ricker wavelets were used for coherent structure detection in a continuous wavelet transform algorithm (PIVlet 1.2). Our bio-inspired study is geared towards understanding whether optimizing the shape of the wavelet kernel will enable better resolution of several low-circulation, multi-scale secondary flow morphologies and whether new insights into the dynamics of arterial secondary flow structures can accordingly be gained. Supported by the National Science Foundation, Grant No. CBET-0828903 and GW Center for Biomimetics and Bioinspired Engineering (COBRE).

  15. Stochastic multi-scale prediction on the apparent elastic moduli of trabecular bone considering uncertainties of biological apatite (BAp) crystallite orientation and image-based modelling.

    PubMed

    Basaruddin, Khairul Salleh; Takano, Naoki; Nakano, Takayoshi

    2015-01-01

    An assessment of the mechanical properties of trabecular bone is important in determining the fracture risk of human bones. Many uncertainty factors contribute to the dispersion of the estimated mechanical properties of trabecular bone. This study was undertaken in order to propose a computational scheme that will be able to predict the effective apparent elastic moduli of trabecular bone considering the uncertainties that are primarily caused by image-based modelling and trabecular stiffness orientation. The effect of image-based modelling which focused on the connectivity was also investigated. A stochastic multi-scale method using a first-order perturbation-based and asymptotic homogenisation theory was applied to formulate the stochastically apparent elastic properties of trabecular bone. The effective apparent elastic modulus was predicted with the introduction of a coefficient factor to represent the variation of bone characteristics due to inter-individual differences. The mean value of the predicted effective apparent Young's modulus in principal axis was found at approximately 460 MPa for respective 15.24% of bone volume fraction, and this is in good agreement with other experimental results. The proposed method may provide a reference for the reliable evaluation of the prediction of the apparent elastic properties of trabecular bone.

  16. Pro-arrhythmogenic effects of CACNA1C G1911R mutation in human ventricular tachycardia: insights from cardiac multi-scale models

    PubMed Central

    Bai, Jieyun; Wang, Kuanquan; Li, Qince; Yuan, Yongfeng; Zhang, Henggui

    2016-01-01

    Mutations in the CACNA1C gene are associated with ventricular tachycardia (VT). Although the CACNA1C mutations were well identified in patients with cardiac arrhythmias, mechanisms by which cardiac arrhythmias are generated in such genetic mutation conditions remain unclear. In this study, we identified a novel mechanism of VT resulted from enhanced repolarization dispersion which is a key factor for arrhythmias in the CACNA1C G1911R mutation using multi-scale computational models of the human ventricle. The increased calcium influx in the mutation prolonged action potential duration (APD), produced steepened action potential duration restitution (APDR) curves as well as augmented membrane potential differences among different cell types during repolarization, increasing transmural dispersion of repolarization (DOR) and the spatial and temporal heterogeneity of cardiac electrical activities. Consequentially, the vulnerability to unidirectional conduction block in response to a premature stimulus increased at tissue level in the G1911R mutation. The increased functional repolarization dispersion anchored reentrant excitation waves in tissue and organ models, facilitating the initiation and maintenance of VT due to less meandering rotor tip. Thus, the increased repolarization dispersion caused by the G1911R mutation is a primary factor that may primarily contribute to the genesis of cardiac arrhythmias in Timothy Syndrome. PMID:27502440

  17. Multi-scale groundwater flow modeling during temperate climate conditions for the safety assessment of the proposed high-level nuclear waste repository site at Forsmark, Sweden

    NASA Astrophysics Data System (ADS)

    Joyce, Steven; Hartley, Lee; Applegate, David; Hoek, Jaap; Jackson, Peter

    2014-09-01

    Forsmark in Sweden has been proposed as the site of a geological repository for spent high-level nuclear fuel, to be located at a depth of approximately 470 m in fractured crystalline rock. The safety assessment for the repository has required a multi-disciplinary approach to evaluate the impact of hydrogeological and hydrogeochemical conditions close to the repository and in a wider regional context. Assessing the consequences of potential radionuclide releases requires quantitative site-specific information concerning the details of groundwater flow on the scale of individual waste canister locations (1-10 m) as well as details of groundwater flow and composition on the scale of groundwater pathways between the facility and the surface (500 m to 5 km). The purpose of this article is to provide an illustration of multi-scale modeling techniques and the results obtained when combining aspects of local-scale flows in fractures around a potential contaminant source with regional-scale groundwater flow and transport subject to natural evolution of the system. The approach set out is novel, as it incorporates both different scales of model and different levels of detail, combining discrete fracture network and equivalent continuous porous medium representations of fractured bedrock.

  18. Multi-scale modelling for the assessment of water quality and land subsidence due to salt layers dissolution

    NASA Astrophysics Data System (ADS)

    Gourdier, Sébastien; Bazargan-Sabet, Behrooz; Quang Vong, Chan

    2016-04-01

    Long term evolution of salt mine depends on mechanical behavior of the material but also on specific conditions like the intrusion of water into working areas. Such phenomenon has been observed in the Nancy Basin (East of France) where brine percolates through access shafts accompanied by significant subsidence at the surface level, bringing about growing societal concerns. In order to understand the mechanisms and kinetics of dissolution of salt inducing the phenom-enon of subsidence, a numerical model is implemented. The circulation of water between the salt layer and the impervious layer induces the creation of dissolution channels. In active disso-lution zones, the channel network constantly evolves: new channels appear with new dissolution zones while others collapse because of their too important dimensions. The model simulates the phenomenon of dissolution at the channel scale first, then at the basin scale. Dissolution channels modeling has been realized using COMSOL Multiphysics® with Darcy's Law and Solute Transport interfaces. At the channel scale, realistic parameters used as input data gave raise to output results con-sistent with the expected range of values for numerical assessment of the transient period and mass fluxes. At the basin scale, initial porosity and hydraulic conductivity fields, related to each other by a cubic law, are assumed to follow a Weibull distribution. From this initial state, the transient model calculates the evolution of porosity with time, taking into account Darcy's velocity as it was formulated by Yao et al. (2014). Progress in dissolution and transport gives rise to the creation of dissolution channels. Channels mechanical behavior is investigated through extending 2D model into 3D one. The calculations show that open channels collapse when they reach a width of approximatively one meter. The results of these investigations are consistent with the in situ measurements, notably with the estimation of the subsidence rate

  19. A multi-scale model for the analysis of the inhomogeneity of elastic properties of DNA biofilm on microcantilevers.

    PubMed

    Zhang, Neng-Hui; Meng, Wei-Lie; Tan, Zou-Qing

    2013-02-01

    In nanoscale diagnostic systems, inhomogeneity in near-surface systems and flexibility in biostructures greatly influence the mechanical/electrical/thermal properties of biosensors and resultant detection signals. This study focuses on inhomogeneity and flexibility of DNA biofilm and characterizes its local interactions and mechanical properties. First, a flexible cylinder model of DNA chain is employed to capture the local geometric deformation characteristics of DNA molecules on microcantilever. In order to describe the inhomogeneous properties of DNA biofilm at thickness direction, the Strey's empirical formula for mesoscopic DNA liquid crystal theory is improved with the assumption of a net charge distribution in film. The model parameters are obtained by curve fitting with experimental data. Second, the biaxial iso-strain compression of thought experiment and the energy conservation law are used to predict macroscopic effective tangent modulus of DNA biofilm in terms of nanoscopic properties of dsDNA, buffer salt concentration. PMID:23228426

  20. A multi-scale problem arising in a model of avian flu virus in a seabird colony

    NASA Astrophysics Data System (ADS)

    Clancy, C. F.; O'Callaghan, M. J. A.; Kelly, T. C.

    2006-12-01

    Understanding the dynamics of epidemics of novel pathogens such as the H5N1 strain of avian influenza is of crucial importance to public and veterinary health as well as wildlife ecology. We model the effect of a new virus on a seabird colony, where no pre-existing Herd Immunity exists. The seabirds in question are so-called K-strategists, i.e. they have a relatively long life expectancy and very low reproductive output. They live in isolated colonies which typically contain tens of thousands of birds. These densely populated colonies, with so many birds competing for nesting space, would seem to provide perfect conditions for the entry and spread of an infection. Yet there are relatively few reported cases of epidemics among these seabirds. We develop a SEIR model which incorporates some of the unusual features of seabird population biology and examine the effects of introducing a pathogen into the colony.

  1. Augmenting Surgery via Multi-scale Modeling and Translational Systems Biology in the Era of Precision Medicine: A Multidisciplinary Perspective.

    PubMed

    Kassab, Ghassan S; An, Gary; Sander, Edward A; Miga, Michael I; Guccione, Julius M; Ji, Songbai; Vodovotz, Yoram

    2016-09-01

    In this era of tremendous technological capabilities and increased focus on improving clinical outcomes, decreasing costs, and increasing precision, there is a need for a more quantitative approach to the field of surgery. Multiscale computational modeling has the potential to bridge the gap to the emerging paradigms of Precision Medicine and Translational Systems Biology, in which quantitative metrics and data guide patient care through improved stratification, diagnosis, and therapy. Achievements by multiple groups have demonstrated the potential for (1) multiscale computational modeling, at a biological level, of diseases treated with surgery and the surgical procedure process at the level of the individual and the population; along with (2) patient-specific, computationally-enabled surgical planning, delivery, and guidance and robotically-augmented manipulation. In this perspective article, we discuss these concepts, and cite emerging examples from the fields of trauma, wound healing, and cardiac surgery. PMID:27015816

  2. Multi-scale Drivers of Variations in Atmospheric Evaporative Demand Based on Observations and Physically-based Modeling

    NASA Astrophysics Data System (ADS)

    Peng, L.; Sheffield, J.; Li, D.

    2015-12-01

    Evapotranspiration (ET) is a key link between the availability of water resources and climate change and climate variability. Variability of ET has important environmental and socioeconomic implications for managing hydrological hazards, food and energy production. Although there have been many observational and modeling studies of ET, how ET has varied and the drivers of the variations at different temporal scales remain elusive. Much of the uncertainty comes from the atmospheric evaporative demand (AED), which is the combined effect of radiative and aerodynamic controls. The inconsistencies among modeled AED estimates and the limited observational data may originate from multiple sources including the limited time span and uncertainties in the data. To fully investigate and untangle the intertwined drivers of AED, we present a spectrum analysis to identify key controls of AED across multiple temporal scales. We use long-term records of observed pan evaporation for 1961-2006 from 317 weather stations across China and physically-based model estimates of potential evapotranspiration (PET). The model estimates are based on surface meteorology and radiation derived from reanalysis, satellite retrievals and station data. Our analyses show that temperature plays a dominant role in regulating variability of AED at the inter-annual scale. At the monthly and seasonal scales, the primary control of AED shifts from radiation in humid regions to humidity in dry regions. Unlike many studies focusing on the spatial pattern of ET drivers based on a traditional supply and demand framework, this study underlines the importance of temporal scales when discussing controls of ET variations.

  3. In silico multi-scale model of transport and dynamic seeding in a bone tissue engineering perfusion bioreactor.

    PubMed

    Spencer, T J; Hidalgo-Bastida, L A; Cartmell, S H; Halliday, I; Care, C M

    2013-04-01

    Computer simulations can potentially be used to design, predict, and inform properties for tissue engineering perfusion bioreactors. In this work, we investigate the flow properties that result from a particular poly-L-lactide porous scaffold and a particular choice of perfusion bioreactor vessel design used in bone tissue engineering. We also propose a model to investigate the dynamic seeding properties such as the homogeneity (or lack of) of the cellular distribution within the scaffold of the perfusion bioreactor: a pre-requisite for the subsequent successful uniform growth of a viable bone tissue engineered construct. Flows inside geometrically complex scaffolds have been investigated previously and results shown at these pore scales. Here, it is our aim to show accurately that through the use of modern high performance computers that the bioreactor device scale that encloses a scaffold can affect the flows and stresses within the pores throughout the scaffold which has implications for bioreactor design, control, and use. Central to this work is that the boundary conditions are derived from micro computed tomography scans of both a device chamber and scaffold in order to avoid generalizations and uncertainties. Dynamic seeding methods have also been shown to provide certain advantages over static seeding methods. We propose here a novel coupled model for dynamic seeding accounting for flow, species mass transport and cell advection-diffusion-attachment tuned for bone tissue engineering. The model highlights the timescale differences between different species suggesting that traditional homogeneous porous flow models of transport must be applied with caution to perfusion bioreactors. Our in silico data illustrate the extent to which these experiments have the potential to contribute to future design and development of large-scale bioreactors.

  4. Multi-scale model of the ionosphere from the combination of modern space-geodetic satellite techniques - project status and first results

    NASA Astrophysics Data System (ADS)

    Schmidt, M.; Hugentobler, U.; Jakowski, N.; Dettmering, D.; Liang, W.; Limberger, M.; Wilken, V.; Gerzen, T.; Hoque, M.; Berdermann, J.

    2012-04-01

    Near real-time high resolution and high precision ionosphere models are needed for a large number of applications, e.g. in navigation, positioning, telecommunications or astronautics. Today these ionosphere models are mostly empirical, i.e., based purely on mathematical approaches. In the DFG project 'Multi-scale model of the ionosphere from the combination of modern space-geodetic satellite techniques (MuSIK)' the complex phenomena within the ionosphere are described vertically by combining the Chapman electron density profile with a plasmasphere layer. In order to consider the horizontal and temporal behaviour the fundamental target parameters of this physics-motivated approach are modelled by series expansions in terms of tensor products of localizing B-spline functions depending on longitude, latitude and time. For testing the procedure the model will be applied to an appropriate region in South America, which covers relevant ionospheric processes and phenomena such as the Equatorial Anomaly. The project connects the expertise of the three project partners, namely Deutsches Geodätisches Forschungsinstitut (DGFI) Munich, the Institute of Astronomical and Physical Geodesy (IAPG) of the Technical University Munich (TUM) and the German Aerospace Center (DLR), Neustrelitz. In this presentation we focus on the current status of the project. In the first year of the project we studied the behaviour of the ionosphere in the test region, we setup appropriate test periods covering high and low solar activity as well as winter and summer and started the data collection, analysis, pre-processing and archiving. We developed partly the mathematical-physical modelling approach and performed first computations based on simulated input data. Here we present information on the data coverage for the area and the time periods of our investigations and we outline challenges of the multi-dimensional mathematical-physical modelling approach. We show first results, discuss problems

  5. Multi-scale reservoir modeling as an integrated assessment tool for geo-sequestration in the San Juan Basin

    USGS Publications Warehouse

    Young, G.; Haerer, D.; Bromhal, G.; Reeves, S.

    2007-01-01

    The Southwestern Regional Partnership on CO2 Sequestration conducted an Enhanced Coalbed Methane (ECBM)/Carbon Storage Pilot in the San Juan Basin as part of the ongoing DOE/NETL Carbon Capture and Storage Program. The primary goal of this pilot is to demonstrate the efficacy of using CO2 to enhance coalbed methane recovery particularly near reservoir abandonment pressure while also evaluating the suitability of coal seams for longer-term carbon storage. Basic geologic models of the coal seams were developed from well logs in the area. Production histories from several surrounding CBM wells were shown. To monitor the injection of up to 75,000 ton of CO2 beginning September 2007, seismic surveys and tiltmeter arrays were utilized. Larger-scale geo-hydrodynamic simulations were used to develop a regional model for the fluid dynamics of the northern San Juan Basin. Smaller-scale reservoir simulations, incorporating available laboratory and field data, were used to develop an improved understanding of reservoir dynamics within the specific 640-acre pilot area. Both modeling scales were critical to assessing the suitability of deploying commercial carbon storage programs throughout the basin. Reservoir characterization results on the optimization of total CO2 injection volume, injection rate over time, and how CO2 is expected to disperse after injection are presented. This is an abstract of a paper presented at the 2007 AIChE Annual Meeting (Salt Lake City, UT 11/4-9/2007).

  6. Data-driven modeling of hydroclimatic trends and soil moisture: Multi-scale data integration and decision support

    NASA Astrophysics Data System (ADS)

    Coopersmith, Evan Joseph

    The techniques and information employed for decision-making vary with the spatial and temporal scope of the assessment required. In modern agriculture, the farm owner or manager makes decisions on a day-to-day or even hour-to-hour basis for dozens of fields scattered over as much as a fifty-mile radius from some central location. Following precipitation events, land begins to dry. Land-owners and managers often trace serpentine paths of 150+ miles every morning to inspect the conditions of their various parcels. His or her objective lies in appropriate resource usage -- is a given tract of land dry enough to be workable at this moment or would he or she be better served waiting patiently? Longer-term, these owners and managers decide upon which seeds will grow most effectively and which crops will make their operations profitable. At even longer temporal scales, decisions are made regarding which fields must be acquired and sold and what types of equipment will be necessary in future operations. This work develops and validates algorithms for these shorter-term decisions, along with models of national climate patterns and climate changes to enable longer-term operational planning. A test site at the University of Illinois South Farms (Urbana, IL, USA) served as the primary location to validate machine learning algorithms, employing public sources of precipitation and potential evapotranspiration to model the wetting/drying process. In expanding such local decision support tools to locations on a national scale, one must recognize the heterogeneity of hydroclimatic and soil characteristics throughout the United States. Machine learning algorithms modeling the wetting/drying process must address this variability, and yet it is wholly impractical to construct a separate algorithm for every conceivable location. For this reason, a national hydrological classification system is presented, allowing clusters of hydroclimatic similarity to emerge naturally from annual

  7. Multi-Scale Particle Size Distributions of Mars, Moon and Itokawa based on a time-maturation dependent fragmentation model

    NASA Astrophysics Data System (ADS)

    Charalambous, C. A.; Pike, W. T.

    2013-12-01

    We present the development of a soil evolution framework and multiscale modelling of the surface of Mars, Moon and Itokawa thus providing an atlas of extra-terrestrial Particle Size Distributions (PSD). These PSDs are profoundly based on a tailoring method which interconnects several datasets from different sites captured by the various missions. The final integrated product is then fully justified through a soil evolution analysis model mathematically constructed via fundamental physical principles (Charalambous, 2013). The construction of the PSD takes into account the macroscale fresh primary impacts and their products, the mesoscale distributions obtained by the in-situ data of surface missions (Golombek et al., 1997, 2012) and finally the microscopic scale distributions provided by Curiosity and Phoenix Lander (Pike, 2011). The distribution naturally extends at the magnitudinal scales at which current data does not exist due to the lack of scientific instruments capturing the populations at these data absent scales. The extension is based on the model distribution (Charalambous, 2013) which takes as parameters known values of material specific probabilities of fragmentation and grinding limits. Additionally, the establishment of a closed-form statistical distribution provides a quantitative description of the soil's structure. Consequently, reverse engineering of the model distribution allows the synthesis of soil that faithfully represents the particle population at the studied sites (Charalambous, 2011). Such representation essentially delivers a virtual soil environment to work with for numerous applications. A specific application demonstrated here will be the information that can directly be extracted for the successful drilling probability as a function of distance in an effort to aid the HP3 instrument of the 2016 Insight Mission to Mars. Pike, W. T., et al. "Quantification of the dry history of the Martian soil inferred from in situ microscopy

  8. The foundational model of anatomy: a template for the symbolic representation of multi-scale physiological functions.

    PubMed

    Cook, D L; Mejino, J L V; Rosse, C

    2004-01-01

    We describe the foundational model of anatomy (FMA), reference ontology for the discipline of human anatomy. Using the semantic structure of the FMA as knowledge representation template, we propose a physiology reference ontology (PRO) as a corresponding ontology for "functional bioinformatics". We envision the PRO as a source vocabulary for building symbolic representations of human physiological states and actions that may ultimately be extensible to other species. We describe the evolving architecture of the PRO, in terms of simple examples based on the anatomical concepts encoded in the FMA. PMID:17271570

  9. Multi-scale First-Principles Modeling of Three-Phase System of Polymer Electrolyte Membrane Fuel Cel

    SciTech Connect

    Brunello, Giuseppe; Choi, Ji; Harvey, David; Jang, Seung

    2012-07-01

    The three-phase system consisting of Nafion, graphite and platinum in the presence of water is studied using molecule dynamics simulation. The force fields describing the molecular interaction between the components in the system are developed to reproduce the energies calculated from density functional theory modeling. The configuration of such complicated three-phase system is predicted through MD simulations. The nanophase-segregation and transport properties are investigated from the equilibrium state. The coverage of the electrolyte on the platinum surface and the dissolution of oxygen are analyzed.

  10. Multi-scale modeling of mycosubtilin lipopeptides at the air/water interface: structure and optical second harmonic generation.

    PubMed

    Loison, Claire; Nasir, Mehmet Nail; Benichou, Emmanuel; Besson, Françoise; Brevet, Pierre-François

    2014-02-01

    Monolayers of the lipopeptide mycosubtilin are studied at the air/water interface. Their structure is investigated using molecular dynamics simulations. All-atom models suggest that the lipopeptide is flexible and aggregates at the interface. To achieve simulation times of several microseconds, a coarse-grained (CG) model based on the MARTINI force field was also used. These CG simulations describe the formation of half-micelles at the interface for surface densities up to 1 lipopeptide per nm(2). In these aggregates, the tyrosine side chain orientation is found to be constrained: on average, its main axis, as defined along the C-OH bond, aligns along the interface normal and points towards the air side. The origin of the optical second harmonic generation (SHG) from mycosubtilin monolayers at the air/water interface is also investigated. The molecular hyperpolarizability of the lipopeptide is obtained from quantum chemistry calculations. The tyrosine side chain contribution to the hyperpolarizability is found to be dominant. The orientation distribution of tyrosine, associated with a dominant hyperpolarizability component along the C-OH bond of the tyrosine, yields a ratio of the susceptibility elements χ((2))(ZZZ)/χ((2))(ZXX) consistent with the experimental measurements recently reported by M. N. Nasir et al. [Phys. Chem. Chem. Phys., 2013, 15, 19919].

  11. Multi-scale modeling of mycosubtilin lipopeptides at the air/water interface: structure and optical second harmonic generation.

    PubMed

    Loison, Claire; Nasir, Mehmet Nail; Benichou, Emmanuel; Besson, Françoise; Brevet, Pierre-François

    2014-02-01

    Monolayers of the lipopeptide mycosubtilin are studied at the air/water interface. Their structure is investigated using molecular dynamics simulations. All-atom models suggest that the lipopeptide is flexible and aggregates at the interface. To achieve simulation times of several microseconds, a coarse-grained (CG) model based on the MARTINI force field was also used. These CG simulations describe the formation of half-micelles at the interface for surface densities up to 1 lipopeptide per nm(2). In these aggregates, the tyrosine side chain orientation is found to be constrained: on average, its main axis, as defined along the C-OH bond, aligns along the interface normal and points towards the air side. The origin of the optical second harmonic generation (SHG) from mycosubtilin monolayers at the air/water interface is also investigated. The molecular hyperpolarizability of the lipopeptide is obtained from quantum chemistry calculations. The tyrosine side chain contribution to the hyperpolarizability is found to be dominant. The orientation distribution of tyrosine, associated with a dominant hyperpolarizability component along the C-OH bond of the tyrosine, yields a ratio of the susceptibility elements χ((2))(ZZZ)/χ((2))(ZXX) consistent with the experimental measurements recently reported by M. N. Nasir et al. [Phys. Chem. Chem. Phys., 2013, 15, 19919]. PMID:24346061

  12. New insights into low-temperature oxidation of propane from synchrotron photoionization mass spectrometry and multi-scale informatics modeling

    SciTech Connect

    Welz, Oliver; Burke, Michael P.; Antonov, Ivan O.; Goldsmith, C. Franklin; Savee, John David; Osborn, David L.; Taatjes, Craig A.; Klippenstein, Stephen J.; Sheps, Leonid

    2015-04-10

    We studied low-temperature propane oxidation at P = 4 Torr and T = 530, 600, and 670 K by time-resolved multiplexed photoionization mass spectrometry (MPIMS), which probes the reactants, intermediates, and products with isomeric selectivity using tunable synchrotron vacuum UV ionizing radiation. The oxidation is initiated by pulsed laser photolysis of oxalyl chloride, (COCl)2, at 248 nm, which rapidly generates a ~1:1 mixture of 1-propyl (n-propyl) and 2-propyl (i-propyl) radicals via the fast Cl + propane reaction. At all three temperatures, the major stable product species is propene, formed in the propyl + O2 reactions by direct HO2 elimination from both n- and i-propyl peroxy radicals. The experimentally derived propene yields relative to the initial concentration of Cl atoms are (20 ± 4)% at 530 K, (55 ± 11)% at 600 K, and (86 ± 17)% at 670 K at a reaction time of 20 ms. The lower yield of propene at low temperature reflects substantial formation of propyl peroxy radicals, which do not completely decompose on the experimental time scale. In addition, C3H6O isomers methyloxirane, oxetane, acetone, and propanal are detected as minor products. Our measured yields of oxetane and methyloxirane, which are coproducts of OH radicals, suggest a revision of the OH formation pathways in models of low-temperature propane oxidation. The experimental results are modeled and interpreted using a multiscale informatics approach, presented in detail in a separate publication (Burke, M. P.; Goldsmith, C. F.; Klippenstein, S. J.; Welz, O.; Huang H.; Antonov I. O.; Savee J. D.; Osborn D. L.; Zádor, J.; Taatjes, C. A.; Sheps, L. Multiscale Informatics for Low-Temperature Propane Oxidation: Further Complexities in Studies of Complex Reactions. J. Phys. Chem A. 2015, DOI: 10.1021/acs.jpca.5b01003). Additionally, we found that the model predicts the time profiles and yields of the experimentally observed primary products well

  13. New insights into low-temperature oxidation of propane from synchrotron photoionization mass spectrometry and multi-scale informatics modeling

    DOE PAGES

    Welz, Oliver; Burke, Michael P.; Antonov, Ivan O.; Goldsmith, C. Franklin; Savee, John David; Osborn, David L.; Taatjes, Craig A.; Klippenstein, Stephen J.; Sheps, Leonid

    2015-04-10

    We studied low-temperature propane oxidation at P = 4 Torr and T = 530, 600, and 670 K by time-resolved multiplexed photoionization mass spectrometry (MPIMS), which probes the reactants, intermediates, and products with isomeric selectivity using tunable synchrotron vacuum UV ionizing radiation. The oxidation is initiated by pulsed laser photolysis of oxalyl chloride, (COCl)2, at 248 nm, which rapidly generates a ~1:1 mixture of 1-propyl (n-propyl) and 2-propyl (i-propyl) radicals via the fast Cl + propane reaction. At all three temperatures, the major stable product species is propene, formed in the propyl + O2 reactions by direct HO2 elimination frommore » both n- and i-propyl peroxy radicals. The experimentally derived propene yields relative to the initial concentration of Cl atoms are (20 ± 4)% at 530 K, (55 ± 11)% at 600 K, and (86 ± 17)% at 670 K at a reaction time of 20 ms. The lower yield of propene at low temperature reflects substantial formation of propyl peroxy radicals, which do not completely decompose on the experimental time scale. In addition, C3H6O isomers methyloxirane, oxetane, acetone, and propanal are detected as minor products. Our measured yields of oxetane and methyloxirane, which are coproducts of OH radicals, suggest a revision of the OH formation pathways in models of low-temperature propane oxidation. The experimental results are modeled and interpreted using a multiscale informatics approach, presented in detail in a separate publication (Burke, M. P.; Goldsmith, C. F.; Klippenstein, S. J.; Welz, O.; Huang H.; Antonov I. O.; Savee J. D.; Osborn D. L.; Zádor, J.; Taatjes, C. A.; Sheps, L. Multiscale Informatics for Low-Temperature Propane Oxidation: Further Complexities in Studies of Complex Reactions. J. Phys. Chem A. 2015, DOI: 10.1021/acs.jpca.5b01003). Additionally, we found that the model predicts the time profiles and yields of the experimentally observed primary products well, and shows satisfactory agreement for products

  14. Multi-scale geospatial agroecosystem modeling: a case study on the influence of soil data resolution on carbon budget estimates.

    PubMed

    Zhang, Xuesong; Sahajpal, Ritvik; Manowitz, David H; Zhao, Kaiguang; Leduc, Stephen D; Xu, Min; Xiong, Wei; Zhang, Aiping; Izaurralde, Roberto C; Thomson, Allison M; West, Tristram O; Post, Wilfred M

    2014-05-01

    The development of effective measures to stabilize atmospheric CO2 concentration and mitigate negative impacts of climate change requires accurate quantification of the spatial variation and magnitude of the terrestrial carbon (C) flux. However, the spatial pattern and strength of terrestrial C sinks and sources remain uncertain. In this study, we designed a spatially-explicit agroecosystem modeling system by integrating the Environmental Policy Integrated Climate (EPIC) model with multiple sources of geospatial and surveyed datasets (including crop type map, elevation, climate forcing, fertilizer application, tillage type and distribution, and crop planting and harvesting date), and applied it to examine the sensitivity of cropland C flux simulations to two widely used soil databases (i.e. State Soil Geographic-STATSGO of a scale of 1:250,000 and Soil Survey Geographic-SSURGO of a scale of 1:24,000) in Iowa, USA. To efficiently execute numerous EPIC runs resulting from the use of high resolution spatial data (56m), we developed a parallelized version of EPIC. Both STATSGO and SSURGO led to similar simulations of crop yields and Net Ecosystem Production (NEP) estimates at the State level. However, substantial differences were observed at the county and sub-county (grid) levels. In general, the fine resolution SSURGO data outperformed the coarse resolution STATSGO data for county-scale crop-yield simulation, and within STATSGO, the area-weighted approach provided more accurate results. Further analysis showed that spatial distribution and magnitude of simulated NEP were more sensitive to the resolution difference between SSURGO and STATSGO at the county or grid scale. For over 60% of the cropland areas in Iowa, the deviations between STATSGO- and SSURGO-derived NEP were larger than 1MgCha(-1)yr(-1), or about half of the average cropland NEP, highlighting the significant uncertainty in spatial distribution and magnitude of simulated C fluxes resulting from

  15. Multi-scale geospatial agroecosystem modeling: a case study on the influence of soil data resolution on carbon budget estimates

    SciTech Connect

    Zhang, Xuesong; Sahajpal, Ritvik; Manowitz, D.; Zhao, Kaiguang; LeDuc, Stephen D.; Xu, Min; Xiong, Wei; Zhang, Aiping; Izaurralde, Roberto C.; Thomson, Allison M.; West, Tristram O.; Post, W. M.

    2014-05-01

    The development of effective measures to stabilize atmospheric CO2 concentration and mitigate negative impacts of climate change requires accurate quantification of the spatial variation and magnitude of the terrestrial carbon (C) flux. However, the spatial pattern and strength of terrestrial C sinks and sources remain uncertain. In this study, we designed a spatially-explicit agroecosystem modeling system by integrating the Environmental Policy Integrated Climate (EPIC) model with multiple sources of geospatial and surveyed datasets (including crop type map, elevation, climate forcing, fertilizer application, tillage type and distribution, and crop planting and harvesting date), and applied it to examine the sensitivity of cropland C flux simulations to two widely used soil databases (i.e. State Soil Geographic-STATSGO of a scale of 1:250,000 and Soil Survey Geographic-SSURGO of a scale of 1:24,000) in Iowa, USA. To efficiently execute numerous EPIC runs resulting from the use of high resolution spatial data (56m), we developed a parallelized version of EPIC. Both STATSGO and SSURGO led to similar simulations of crop yields and Net Ecosystem Production (NEP) estimates at the State level. However, substantial differences were observed at the county and sub-county (grid) levels. In general, the fine resolution SSURGO data outperformed the coarse resolution STATSGO data for county-scale crop-yield simulation, and within STATSGO, the area-weighted approach provided more accurate results. Further analysis showed that spatial distribution and magnitude of simulated NEP were more sensitive to the resolution difference between SSURGO and STATSGO at the county or grid scale. For over 60% of the cropland areas in Iowa, the deviations between STATSGO- and SSURGO-derived NEP were larger than 1MgCha(-1)yr(-1), or about half of the average cropland NEP, highlighting the significant uncertainty in spatial distribution and magnitude of simulated C fluxes resulting from

  16. Multi-Scale, Multimedia Modeling With Pangea: Local To Global Evaluation Of The Human Health Impacts Of Emissions From Coal Power To Bar Soap

    NASA Astrophysics Data System (ADS)

    Henderson, A. D.; Wannaz, C.; Jolliet, O.

    2012-12-01

    Environmental impact and risk assessments of chemical emissions have often been local, regional, or global. However, linking such models is difficult, hindering comparison of impacts across these scales. Such links are important, as local risk assessments might only account for a fraction of global impacts for some compounds. For example, 90% of the emissions of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/F) might be deposited more than 100km away from sources (1). There is therefore a need for a flexible, fate/transport, and multi-pathway exposure model that spans scales. We have developed a model, called Pangea, which models the intake of emissions as the intake fraction - the fraction of an emission that is ultimately taken in by the population, from local to global scale. Studies of a single-source emission in various parts of the world (e.g., Europe or East Asia) provide critical insight for effective understanding of geospatial distribution of impacts. The model is spatially explicit, building on a set of environmental process models (EPMs) to cover a range of multimedia exposure pathways. These EPMs describe interactions between environmental compartments, as well as internal processes such as degradation. Atmosphere, fresh water networks, oceans, sediments, and land cover data are projected onto multi-scale grids at runtime. Multi-scale refinement is based on factors including distance from the source and population density, creating a computationally effficient grid that can be adapted to the specific needs of individual studies. Spatial analysis of the intake of an emission of 2,3,7,8-TCDD from northern France shows that most of the impact takes place in western Germany, due to the high population density of that region and the prevailing wind direction. Emissions in highly populated area or area with high agriculture production intensities in China and Japan may lead to even higher intake fractions. Results indicate that for

  17. Evaluating WRF-Chem multi-scale model in simulating aerosol radiative properties over the tropics – A case study over India

    SciTech Connect

    Seethala, C.; Pandithurai, G.; Fast, Jerome D.; Polade, Suraj D.; Reddy, M. S.; Peckham, Steven E.

    2012-01-24

    We utilized WRF-Chem multi-scale model to simulate the regional distribution of aerosols, optical properties and its effect on radiation over India for a winter month. The model is evaluated using measurements obtained from upper-air soundings, AERONET sun photometers, various satellite instruments, and pyranometers operated by the Indian Meteorological Department. The simulated downward shortwave flux was overestimated when the effect of aerosols on radiation and clouds was neglected. Downward shortwave radiation from a simulation that included aerosol-radiation interaction processes was 5 to 25 Wm{sup -2} closer to the observations, while a simulation that included aerosol-cloud interaction processes were another 1 to 20 Wm{sup -2} closer to the observations. For the few observations available, the model usually underestimated particulate concentration. This is likely due to turbulent mixing, transport errors and the lack of secondary organic aerosol treatment in the model. The model efficiently captured the broad regional hotspots such as high aerosol optical depth over Indo-Gangetic basin as well as the northwestern and southern part of India. The regional distribution of aerosol optical depth compares well with AVHRR aerosol optical depth and the TOMS aerosol index. The magnitude and wavelength-dependence of simulated aerosol optical depth was also similar to the AERONET observations across India. Differences in surface shortwave radiation between simulations that included and neglected aerosol-radiation interactions were as high as -25 Wm{sup -2}, while differences in surface shortwave radiation between simulations that included and neglect aerosol-radiation-cloud interactions were as high as -30 Wm{sup -2}. The spatial variations of these differences were also compared with AVHRR observation. This study suggests that the model is able to qualitatively simulate the impact of aerosols on radiation over India; however, additional measurements of particulate

  18. Evolution of Tides and Tidal Dissipation Over the Past 26,000 Years Using a Multi-Scale Model of Global Barotropic Tides

    NASA Astrophysics Data System (ADS)

    Salehipour, H.; Peltier, W. R.

    2014-12-01

    In this paper we will describe the results obtained through integration of a further refined version of the truly global barotropic tidal model of Salehipour et al. (Ocean Modell., 69, 2013) using the most recent reconstruction of ice-age bathymetric conditions as embodied in the recently constructed ICE-6G_C (VM5a) model of Peltier et al. (JGR-Solid Earth, in press, 2014). Our interest is in the spatial and temporal evolution of tidal amplitude, phase and dissipation from the Last Glacial Maximum (LGM) 26,000 years ago until the present. The state-of-the-art higher order nonlinear tidal model of Salehipour et al. (2013) includes a highly parallelized multi-scale framework in which an unstructured tessellation of the global ocean enables extensive local refinement around regions of interest such as the Hawaiian Ridge, the Brazil Basin and the Southern Ocean. At LGM, features such as the Patagonian Shelf were fully exposed land which during the deglaciation process would have been flooded leading to significant changes of tidal range along the evolving coastline. In the further development of this model we have included the fully iterated treatment of the influence of gravitational self-attraction and loading as in, e.g. Egbert et al. (JGR-Oceans, 109, 2004). The treatment of the dissipation of the barotropic tide through dissipation of the internal tide has also been significantly improved. Our paleobathymetry and coastline data sets extend from LGM to present at 500 year intervals and constitute a significant refinement of the widely employed ICE-5G (VM2) model of Peltier (Annu. Rev. Earth Planet. Sci., 32, 2004). Our results will be compared with those recently published by Green & Nycander (JPO, 43, 2013) and Wilmes & Green (JGR-Oceans, 119, 2014) as well as with the earlier results of Griffiths & Peltier (GRL, 35, 2008; J. Clim., 22, 2009).

  19. Role of band 3 in the erythrocyte membrane structural changes under thermal fluctuations -multi scale modeling considerations.

    PubMed

    Pajic-Lijakovic, Ivana

    2015-12-01

    An attempt was made to discuss and connect various modeling approaches on various time and space scales which have been proposed in the literature in order to shed further light on the erythrocyte membrane rearrangement caused by the cortex-lipid bilayer coupling under thermal fluctuations. Roles of the main membrane constituents: (1) the actin-spectrin cortex, (2) the lipid bilayer, and (3) the trans membrane protein band 3 and their course-consequence relations were considered in the context of the cortex non linear stiffening and corresponding anomalous nature of energy dissipation. The fluctuations induce alternating expansion and compression of the membrane parts in order to ensure surface and volume conservation. The membrane structural changes were considered within two time regimes. The results indicate that the cortex non linear stiffening and corresponding anomalous nature of energy dissipation are related to the spectrin flexibility distribution and the rate of its changes. The spectrin flexibility varies from purely flexible to semi flexible. It is influenced by: (1) the number of band 3 molecules attached to single spectrin filaments, and (2) phosphorylation of the actin-junctions. The rate of spectrin flexibility changes depends on the band 3 molecules rearrangement.

  20. Measurement, modeling and perception of painted surfaces: A Multi-scale Analysis of the Touch-up Problem

    NASA Astrophysics Data System (ADS)

    Kalghatgi, Suparna Kishore

    used as base data towards development of a psychophysical model that relates physical differences in paint formulation and application methods to visual differences in surface appearance.

  1. Multi-scale investigation of fine-sediment ingress in gravel-bed rivers using experiments and numerical modelling

    NASA Astrophysics Data System (ADS)

    Lamparter, Gabriele; Collins, Adrian; Nicholas, Andrew

    2015-04-01

    Increased suspended sediment loads in gravel-bed rivers, potentially leading to clogging of the pores in the river bed, is a problem acknowledged since at least the 1980s. Early research was concerned with declining salmonid production along the North American Pacific coast due to siltation processes. Since then, research has expanded and includes a wider geographical and ecological coverage. Despite this long history of research into gravel-clogging by fine sediment, the relationship between enhanced suspended sediment loads and sediment ingress is still poorly quantified. The research presented here seeks to address this gap and has a two scale approach to improve the quantification of fine-sediment ingress into river gravels under a range of flow, fine sediment and gravel framework conditions. Laboratory scale flume experiments mimicking natural conditions were used to measure flow and the character of fine sediment both above and ingressing into custom-made basket traps. At a larger scale, the same basket traps were installed in a field setting (the gravel-bed River Culm in South-West England) in three river reaches, in conjunction with continuous monitoring of suspended sediment concentration and flow discharge (to estimate sediment loads). The data were evaluated with regards to the Krone formulation for deposition (Krone, 1962), an equation generally believed to include the main physical determinants driving fine-sediment deposition. The formulation states that rise in suspended sediment concentration, settling velocity and also decline of flow velocity or bed shear stress all lead to an increase in suspended sediment deposition. This evaluation was achieved by setting up a numerical model, which was initially applied to the flume experiments and subsequently up-scaled to the field scale. Data generated by both the flume and the field experiments do not agree well with the predictions of the Krone formulations. This agreement was especially weak for fine

  2. Strategies of Eradicating Glioma Cells: A Multi-Scale Mathematical Model with MiR-451-AMPK-mTOR Control

    PubMed Central

    Kim, Yangjin; Powathil, Gibin; Kang, Hyunji; Trucu, Dumitru; Kim, Hyeongi; Lawler, Sean; Chaplain, Mark

    2015-01-01

    The cellular dispersion and therapeutic control of glioblastoma, the most aggressive type of primary brain cancer, depends critically on the migration patterns after surgery and intracellular responses of the individual cancer cells in response to external biochemical and biomechanical cues in the microenvironment. Recent studies have shown that a particular microRNA, miR-451, regulates downstream molecules including AMPK and mTOR to determine the balance between rapid proliferation and invasion in response to metabolic stress in the harsh tumor microenvironment. Surgical removal of main tumor is inevitably followed by recurrence of the tumor due to inaccessibility of dispersed tumor cells in normal brain tissue. In order to address this multi-scale nature of glioblastoma proliferation and invasion and its response to conventional treatment, we propose a hybrid model of glioblastoma that analyses spatio-temporal dynamics at the cellular level, linking individual tumor cells with the macroscopic behaviour of cell organization and the microenvironment, and with the intracellular dynamics of miR-451-AMPK-mTOR signaling within a tumour cell. The model identifies a key mechanism underlying the molecular switches between proliferative phase and migratory phase in response to metabolic stress and biophysical interaction between cells in response to fluctuating glucose levels in the presence of blood vessels (BVs). The model predicts that cell migration, therefore efficacy of the treatment, not only depends on oxygen and glucose availability but also on the relative balance between random motility and strength of chemoattractants. Effective control of growing cells near BV sites in addition to relocalization of invisible migratory cells back to the resection site was suggested as a way of eradicating these migratory cells. PMID:25629604

  3. Impacts of transported background ozone on California air quality during the ARCTAS-CARB period - a multi-scale modeling study

    NASA Astrophysics Data System (ADS)

    Huang, M.; Carmichael, G. R.; Adhikary, B.; Spak, S. N.; Kulkarni, S.; Cheng, Y.; Wei, C.; Tang, Y.; Parrish, D. D.; Oltmans, S. J.; D'Allura, A.; Kaduwela, A.; Cai, C.; Weinheimer, A. J.; Wong, M.; Pierce, R. B.; Al-Saadi, J. A.; Streets, D. G.; Zhang, Q.

    2010-05-01

    Multi-scale tracer and full-chemistry simulations with the STEM atmospheric chemistry model are used to analyze the effects of transported background ozone (O3) from the eastern Pacific on California air quality during the ARCTAS-CARB experiment conducted in June 2008. Previous work has focused on the importance of long-range transport of O3 to North America air quality in springtime. However during this summer experiment the long-range transport of O3 is also shown to be important. Simulated and observed O3 transport patterns from the coast to inland northern California are shown to vary based on meteorological conditions and the oceanic O3 profiles, which are strongly episodically affected by Asian inflows. Analysis of the correlations of O3 at various altitudes above the coastal site at Trinidad Head and at a downwind surface site in northern California, show that under long-range transport events, high O3 air-masses (O3>60 ppb) at altitudes between about 2 and 4 km can be transported inland and can significantly influence surface O3 20-30 h later. These results show the importance of characterizing the vertical structure of the lateral boundary conditions (LBC) needed in air quality simulations. The importance of the LBC on O3 prediction during this period is further studied through a series of sensitivity studies using different forms of LBC. It is shown that the use of the LBC downscaled from RAQMS global model that assimilated MLS and OMI data improves the model performance. We also show that the predictions can be further improved through the use of LBC based on NASA DC-8 airborne observations during the ARCTAS-CARB experiment. These results indicate the need to develop observational strategies to improve the representation of the vertical and temporal variations in the air over the eastern Pacific.

  4. Changing stream water sources from climate-exacerbated insect infestation in forested watersheds: a combined field and multi-scale modeling analysis.

    NASA Astrophysics Data System (ADS)

    Maxwell, R. M.; Bearup, L. A.; Penn, C. A.; Jefferson, J.; Engdahl, N. B.

    2014-12-01

    Changing climate, including warmer temperatures and drought conditions, has intensified mountain pine beetle infestation in the Rocky Mountains of North America, resulting in tree death over the last decade that is unprecedented in recorded history. The subsequent perturbation to tree-scale water budget processes such as interception, transpiration, and evaporation often combine non-uniformly and produce variable catchment-scale responses. Potentially offsetting perturbations such as decreased transpiration with tree death and increased exposure and evaporation with needle fall can produce changes in peak streamflow and water yield that are undetectable above typical interannual variability. These combined perturbations, however, may change streamflow generating processes and water sources that impact water quality in important mountain headwater streams. To determine the potential impact of widespread land cover change on catchment contributions to streamflow, this study combines a chemical and isotopic separation analysis using paired watersheds and pre-infestation controls with a multi-scale modeling approach (from hillslope to headwaters systems) that determines changes in water stores and fluxes between canopy, land-surface, groundwater and streamflow. Field observations and chemical hydrograph separation analysis suggest that groundwater contributions to streamflow increase with recent insect infestation, as transpiration ceases to remove water from the subsurface but potentially increased ground evaporation removes water from the land and subsurface with relative uniformity. Comparing these field observations to hillslope models provides additional spatial and temporal controls on inherently challenging field heterogeneities as well as a way of testing the influence of natural properties such as precipitation and topography on perturbations to streamflow partitioning from insect infestation. At larger scales, watershed models demonstrate how other factors

  5. Multi-scale enhancement of climate prediction over land by increasing the model sensitivity to vegetation variability in EC-Earth

    NASA Astrophysics Data System (ADS)

    Alessandri, Andrea; Catalano, Franco; De Felice, Matteo; Van Den Hurk, Bart; Doblas Reyes, Francisco; Boussetta, Souhail; Balsamo, Gianpaolo; Miller, Paul

    2016-04-01

    The EC-Earth earth system model has been recently developed to include the dynamics of vegetation. In its original formulation, vegetation variability is simply operated by the Leaf Area Index (LAI), which affects climate basically by changing the vegetation physiological resistance to evapotranspiration. This coupling has been found to have only a weak effect on the surface climate modeled by EC-Earth. In reality, the effective sub-grid vegetation fractional coverage will vary seasonally and at interannual time-scales in response to leaf-canopy growth, phenology and senescence. Therefore it affects biophysical parameters such as the albedo, surface roughness and soil field capacity. To adequately represent this effect in EC-Earth, we included an exponential dependence of the vegetation cover on the LAI. By comparing two sets of simulations performed with and without the new variable fractional-coverage parameterization, spanning retrospective predictions at the decadal (5-years), seasonal and sub-seasonal time-scales, we show for the first time a significant multi-scale enhancement of vegetation impacts in climate simulation and prediction over land. Particularly large effects at multiple time scales are shown over boreal winter middle-to-high latitudes over Canada, West US, Eastern Europe, Russia and eastern Siberia due to the implemented time-varying shadowing effect by tree-vegetation on snow surfaces. Over Northern Hemisphere boreal forest regions the improved representation of vegetation cover tends to correct the winter warm biases, improves the climate change sensitivity, the decadal potential predictability as well as the skill of forecasts at seasonal and sub-seasonal time-scales. Significant improvements of the prediction of 2m temperature and rainfall are also shown over transitional land surface hot spots. Both the potential predictability at decadal time-scale and seasonal-forecasts skill are enhanced over Sahel, North American Great Plains, Nordeste

  6. Multi-scale enhancement of climate prediction over land by increasing the model sensitivity to vegetation variability in EC-Earth

    NASA Astrophysics Data System (ADS)

    Alessandri, Andrea; Catalano, Franco; De Felice, Matteo; Van Den Hurk, Bart; Doblas Reyes, Francisco; Boussetta, Souhail; Balsamo, Gianpaolo; Miller, Paul A.

    2016-10-01

    The EC-Earth earth system model has been recently developed to include the dynamics of vegetation. In its original formulation, vegetation variability is simply operated by the Leaf Area Index (LAI), which affects climate basically by changing the vegetation physiological resistance to evapotranspiration. This coupling has been found to have only a weak effect on the surface climate modeled by EC-Earth. In reality, the effective sub-grid vegetation fractional coverage will vary seasonally and at interannual time-scales in response to leaf-canopy growth, phenology and senescence. Therefore it affects biophysical parameters such as the albedo, surface roughness and soil field capacity. To adequately represent this effect in EC-Earth, we included an exponential dependence of the vegetation cover on the LAI. By comparing two sets of simulations performed with and without the new variable fractional-coverage parameterization, spanning from centennial (twentieth century) simulations and retrospective predictions to the decadal (5-years), seasonal and weather time-scales, we show for the first time a significant multi-scale enhancement of vegetation impacts in climate simulation and prediction over land. Particularly large effects at multiple time scales are shown over boreal winter middle-to-high latitudes over Canada, West US, Eastern Europe, Russia and eastern Siberia due to the implemented time-varying shadowing effect by tree-vegetation on snow surfaces. Over Northern Hemisphere boreal forest regions the improved representation of vegetation cover tends to correct the winter warm biases, improves the climate change sensitivity, the decadal potential predictability as well as the skill of forecasts at seasonal and weather time-scales. Significant improvements of the prediction of 2 m temperature and rainfall are also shown over transitional land surface hot spots. Both the potential predictability at decadal time-scale and seasonal-forecasts skill are enhanced over

  7. Study of Multi-Scale Cloud Processes Over the Tropical Western Pacific Using Cloud-Resolving Models Constrained by Satellite Data

    SciTech Connect

    Dudhia, Jimy

    2013-03-12

    Clouds in the tropical western Pacific are an integral part of the large scale environment. An improved understanding of the multi-scale structure of clouds and their interactions with the environment is critical to the ARM (Atmospheric Radiation Measurement) program for developing and evaluating cloud parameterizations, understanding the consequences of model biases, and providing a context for interpreting the observational data collected over the ARM Tropical Western Pacific (TWP) sites. Three-dimensional cloud resolving models (CRMs) are powerful tools for developing and evaluating cloud parameterizations. However, a significant challenge in using CRMs in the TWP is that the region lacks conventional data, so large uncertainty exists in defining the large-scale environment for clouds. This project links several aspects of the ARM program, from measurements to providing improved analyses, and from cloud-resolving modeling to climate-scale modeling and parameterization development, with the overall objective to improve the representations of clouds in climate models and to simulate and quantify resolved cloud effects on the large-scale environment. Our objectives will be achieved through a series of tasks focusing on the use of the Weather Research and Forecasting (WRF) model and ARM data. Our approach includes: -- Perform assimilation of COSMIC GPS radio occultation and other satellites products using the WRF Ensemble Kalman Filter assimilation system to represent the tropical large-scale environment at 36 km grid resolution. This high-resolution analysis can be used by the community to derive forcing products for single-column models or cloud-resolving models. -- Perform cloud-resolving simulations using WRF and its nesting capabilities, driven by the improved regional analysis and evaluate the simulations against ARM datasets such as from TWP-ICE to optimize the microphysics parameters for this region. A cirrus study (Mace and co-authors) already exists for

  8. Earthquake sequence simulation of a multi-scale asperity model following rate and state friction - occurrence of large earthquakes by cascade up vs. own nucleation

    NASA Astrophysics Data System (ADS)

    Noda, H.; Nakatani, M.; Hori, T.

    2012-12-01

    Seismological observations [e.g., Abercrombie and Rice, 2005] suggest that a larger earthquake has larger fracture energy Gc. One way to realize such scaling is to assume a hierarchical patchy distribution of Gc on a fault; there are patches of different sizes with different Gc so that a larger patch has larger Gc. Ide and Aochi [2005] conducted dynamic rupture simulations with such a distribution of weakening distance Dc in a linear slip-weakening law, initiating ruptures on the smallest patch which sometimes grow up by cascading into a larger scale. They suggested that the initial phase of a large earthquake is indistinguishable from that of a small earthquake. In the present study we simulate a similar multi-scale asperity model but following rate and state friction (RSF), where stress and strength distribution resulting from the history of coseismic and aseismic slip influences the way of rupture initiation, growth, and arrest of a forthcoming earthquake. Multi-scale asperities were represented by a distribution of the state evolution distance dc in the aging version of RSF evolution law. Numerical scheme adopted [Noda and Lapsuta, 2010] is fully dynamic and 3D. We have modeled a circular rate-weakening patch, Patch L (radius R), which has a smaller patch, Patch S (radius r), in it by the rim. The ratio of the radii α = R/r is the amount of the gap between two scales. Patch L and Patch S respectively have nucleation sizes Rc and rc. The same brittleness β = R/Rc = r/rc is assumed for simplicity. We shall call an earthquake which ruptures only Patch S as an S-event, and one which ruptures Patch L, an L-event. We have conducted a series of simulations with α from 2 to 5 while keeping β = 3 until the end of the 20th L-event. If the patch S was relatively large (α = 2 and 2.5), only L-events occurred and they always dynamically cascaded up from a patch S rupture following small quasi-static nucleation there. If the patch S was small enough (α = 5), in

  9. An integrated multi-scale hydrogeological model for performance and safety assessment of French geological high level and long live radwaste disposal in clay formation

    NASA Astrophysics Data System (ADS)

    Benabderrahmane, H.; Cornaton, F. J.; Kerrou, J.

    2009-12-01

    A deep geological repository of high level and long live radwaste requires sound understanding of the far field and near field groundwater flow and transport properties. Andra, French National radioactive waste management Agency is developing since last 15 years, an integrated multi-scale hydrogeological model of whole Paris basin of 200'000 Km2 area (regional scale) to produce a regional flow field associated to groundwater behavior. It includes locally the Meuse / Haute Marne clay site of about 250 Km2 area in the eastern part of Paris basin that was chosen for the emplacement of a repository. Callovo-Oxfordian as host formation is a clay layer characterized by very low permeability, a mean thickness of 130 m at about 500 m depth and is embedded by calcareous formations as aquifers (Dogger and Oxfordian). The hydrogeological conceptual model is based on stratigraphic and petrophysic modeling of the Paris basin and is accounting for the sound structural, geological, hydrogeological and geochemical data in an integrated way. At Paris basin scale, the model is a multilayer system of 27 layers (hydrogeological units) from Trias to Tertiary. A refinement at local scale of the site defines 27 hydro-geological units from Trias to Portlandian within an area of 1800 Km2. Based on sound data acquisition from borehole and seismic campaigns performed by Andra, regional faults, minor and diffuse fractures are considered. A structural and petrophysical representation of the transition zone between the Paris basin scale and site scale, as well as a better handling of surface flow boundary conditions are considered. Finite element flow and transport simulator Ground Water code (GW) is used to solve for groundwater flow at steady-state in a 1.8 Million nodes model, considering current climatic conditions. The model is calibrated against about 1250 hydraulic head measurements, and results in maximum absolute hydraulic head differences of 20 meters at the regional scale and 5

  10. Multi-scale Shock Technique

    2009-08-01

    The code to be released is a new addition to the LAMMPS molecular dynamics code. LAMMPS is developed and maintained by Sandia, is publicly available, and is used widely by both natioanl laboratories and academics. The new addition to be released enables LAMMPS to perform molecular dynamics simulations of shock waves using the Multi-scale Shock Simulation Technique (MSST) which we have developed and has been previously published. This technique enables molecular dynamics simulations of shockmore » waves in materials for orders of magnitude longer timescales than the direct, commonly employed approach.« less

  11. Multi-scale integrated structural and aeromagnetic analysis to guide tectonic models: An example from the eastern Musgrave Province, Central Australia

    NASA Astrophysics Data System (ADS)

    Aitken, Alan R. A.; Betts, Peter G.

    2009-10-01

    In many polydeformed Precambrian provinces, the understanding of their tectonic history is limited by insufficient exposure, which leads to difficulty in developing links between local and regional architecture, and results in poorly constrained models of their regional-scale architecture. High-resolution aeromagnetic data allows interpretation and modelling at a scale comparable to structural mapping, and by integrating these methods, these links can be developed with high confidence. As an example, we integrate structural mapping, aeromagnetic data interpretation and 3D magnetic inversions in a multi-scale structural analysis of the polydeformed eastern Musgrave Province in central Australia. Deformation during the ca. 1200 Ma Musgravian Orogeny is characterised by an originally northeast-trending structural grain defined by shear zones and tight to isoclinal folds at all scales. 3D magnetic inversion models of syn-to-post Musgravian granites indicate that this structural grain is predominantly west dipping. This architecture suggests that a northeast-oriented fold and thrust belt developed as a result of northwest-southeast compression in central Australia during the Musgravian Orogeny. The next deformation event is characterised by an array of originally east-southeast trending shear zones that truncate and offset the Musgravian structural grain with apparent dextral displacements of up to 1 km. These shear zones are commonly co-located with mafic and granitic dykes, suggesting a dilational origin, and they are interpreted to have initiated under northeast-southwest extension during the ca. 1080 Ma Giles Event. The architecture of these two Mesoproterozoic events was later extensively overprinted by two deformation events during the Pan-African aged (ca. 550 Ma) Petermann Orogeny. The first is characterised by the widespread reactivation of Mesoproterozoic structures, resulting in a network of shear zones of variable orientation, and the second is characterised

  12. A multi-directional and multi-scale roughness filter to detect lineament segments on digital elevation models - analyzing spatial objects in R

    NASA Astrophysics Data System (ADS)

    Baumann, Sebastian; Robl, Jörg; Wendt, Lorenz; Willingshofer, Ernst; Hilberg, Sylke

    2016-04-01

    Automated lineament analysis on remotely sensed data requires two general process steps: The identification of neighboring pixels showing high contrast and the conversion of these domains into lines. The target output is the lineaments' position, extent and orientation. We developed a lineament extraction tool programmed in R using digital elevation models as input data to generate morphological lineaments defined as follows: A morphological lineament represents a zone of high relief roughness, whose length significantly exceeds the width. As relief roughness any deviation from a flat plane, defined by a roughness threshold, is considered. In our novel approach a multi-directional and multi-scale roughness filter uses moving windows of different neighborhood sizes to identify threshold limited rough domains on digital elevation models. Surface roughness is calculated as the vertical elevation difference between the center cell and the different orientated straight lines connecting two edge cells of a neighborhood, divided by the horizontal distance of the edge cells. Thus multiple roughness values depending on the neighborhood sizes and orientations of the edge connecting lines are generated for each cell and their maximum and minimum values are extracted. Thereby negative signs of the roughness parameter represent concave relief structures as valleys, positive signs convex relief structures as ridges. A threshold defines domains of high relief roughness. These domains are thinned to a representative point pattern by a 3x3 neighborhood filter, highlighting maximum and minimum roughness peaks, and representing the center points of lineament segments. The orientation and extent of the lineament segments are calculated within the roughness domains, generating a straight line segment in the direction of least roughness differences. We tested our algorithm on digital elevation models of multiple sources and scales and compared the results visually with shaded relief map

  13. Hands-on, online, and workshop-based K-12 weather and climate education resources from the Center for Multi-scale Modeling of Atmospheric Processes

    NASA Astrophysics Data System (ADS)

    Foster, S. Q.; Johnson, R. M.; Randall, D. A.; Denning, A.; Burt, M. A.; Gardiner, L.; Genyuk, J.; Hatheway, B.; Jones, B.; La Grave, M. L.; Russell, R. M.

    2009-12-01

    The need for improving the representation of cloud processes in climate models has been one of the most important limitations of the reliability of climate-change simulations. Now in its fourth year, the National Science Foundation-funded Center for Multi-scale Modeling of Atmospheric Processes (CMMAP) at Colorado State University (CSU) is addressing this problem through a revolutionary new approach to representing cloud processes on their native scales, including the cloud-scale interaction processes that are active in cloud systems. CMMAP has set ambitious education and human-resource goals to share basic information about the atmosphere, clouds, weather, climate, and modeling with diverse K-12 and public audiences. This is accomplished through collaborations in resource development and dissemination between CMMAP scientists, CSU’s Little Shop of Physics (LSOP) program, and the Windows to the Universe (W2U) program at University Corporation for Atmospheric Research (UCAR). Little Shop of Physics develops new hands on science activities demonstrating basic science concepts fundamental to understanding atmospheric characteristics, weather, and climate. Videos capture demonstrations of children completing these activities which are broadcast to school districts and public television programs. CMMAP and LSOP educators and scientists partner in teaching a summer professional development workshops for teachers at CSU with a semester's worth of college-level content on the basic physics of the atmosphere, weather, climate, climate modeling, and climate change, as well as dozens of LSOP inquiry-based activities suitable for use in classrooms. The W2U project complements these efforts by developing and broadly disseminating new CMMAP-related online content pages, animations, interactives, image galleries, scientists’ biographies, and LSOP videos to K-12 and public audiences. Reaching nearly 20 million users annually, W2U is highly valued as a curriculum enhancement

  14. Advances in Sun-Earth Connection Modeling

    NASA Astrophysics Data System (ADS)

    Ganguli, S. B.; Gavrishchaka, V. V.

    2003-06-01

    Space weather forecasting is a focus of a multidisciplinary research effort motivated by a sensitive dependence of many modern technologies on geospace conditions. Adequate understanding of the physics of the Sun-Earth connection and associated multi-scale magnetospheric and ionospheric processes is an essential part of this effort. Modern physical simulation models such as multimoment multifluid models with effective coupling from small-scale kinetic processes can provide valuable insight into the role of various physical mechanisms operating during geomagnetic storm/substorm activity. However, due to necessary simplifying assumptions, physical models are still not well suited for accurate real-time forecasting. Complimentary approach includes data-driven models capable of efficient processing of multi-scale spatio-temporal data. However, the majority of advanced nonlinear algorithms, including neural networks (NN), can encounter a set of problems called dimensionality curse when applied to high-dimensional data. Forecasting of rare/extreme events such as large geomagnetic storms/substorms is of the most practical importance but is also very challenging for many existing models. A very promising algorithm that combines the power of the best nonlinear techniques and tolerance to high-dimensional and incomplete data is support vector machine (SVM). We have summarized advantages of the SVM and described a hybrid model based on SVM and extreme value theory (EVT) for rare event forecasting. Results of the SVM application to substorm forecasting and future directions are discussed.

  15. Advancing Ecological Models to Compare Scale in Multi-Level Educational Change

    ERIC Educational Resources Information Center

    Woo, David James

    2016-01-01

    Education systems as units of analysis have been metaphorically likened to ecologies to model change. However, ecological models to date have been ineffective in modelling educational change that is multi-scale and occurs across multiple levels of an education system. Thus, this paper advances two innovative, ecological frameworks that improve on…

  16. Impacts of transported background ozone on California air quality during the ARCTAS-CARB period - a multi-scale modeling study

    NASA Astrophysics Data System (ADS)

    Huang, M.; Carmichael, G. R.; Adhikary, B.; Spak, S. N.; Kulkarni, S.; Cheng, Y. F.; Wei, C.; Tang, Y.; Parrish, D. D.; Oltmans, S. J.; D'Allura, A.; Kaduwela, A.; Cai, C.; Weinheimer, A. J.; Wong, M.; Pierce, R. B.; Al-Saadi, J. A.; Streets, D. G.; Zhang, Q.

    2010-07-01

    Multi-scale tracer and full-chemistry simulations with the STEM atmospheric chemistry model are used to analyze the effects of transported background ozone (O3) from the eastern Pacific on California air quality during the ARCTAS-CARB experiment conducted in June, 2008. Previous work has focused on the importance of long-range transport of O3 to North America air quality in springtime. However during this summer experiment the long-range transport of O3 is also shown to be important. Simulated and observed O3 transport patterns from the coast to inland northern California are shown to vary based on meteorological conditions and the O3 profiles over the oceans, which are strongly episodically affected by Asian inflows. Analysis of the correlations of O3 at various altitudes above the coastal site at Trinidad Head and at a downwind surface site in northern California, show that under long-range transport events, high O3 air-masses (O3>60 ppb) at altitudes between about 2 and 4 km can be transported inland and can significantly influence surface O3 20-30 h later. These results show the importance of characterizing the vertical structure of the lateral boundary conditions (LBC) needed in air quality simulations. The importance of the LBC on O3 prediction during this period is further studied through a series of sensitivity studies using different forms of LBC. It is shown that the use of the LBC downscaled from RAQMS global model that assimilated MLS and OMI data improves the model performance. We also show that the predictions can be further improved through the use of LBC based on NASA DC-8 airborne observations during the ARCTAS-CARB experiment. These results indicate the need to develop observational strategies to provide information on the three-dimensional nature of pollutant distributions, in order to improve our capability to predict pollution levels and to better quantify the influence of these Asian inflows on the US west coast air quality.

  17. Multi-scale gravity and cosmology

    SciTech Connect

    Calcagni, Gianluca

    2013-12-01

    The gravitational dynamics and cosmological implications of three classes of recently introduced multi-scale spacetimes (with, respectively, ordinary, weighted and q-derivatives) are discussed. These spacetimes are non-Riemannian: the metric structure is accompanied by an independent measure-differential structure with the characteristics of a multi-fractal, namely, different dimensionality at different scales and, at ultra-short distances, a discrete symmetry known as discrete scale invariance. Under this minimal paradigm, five general features arise: (a) the big-bang singularity can be replaced by a finite bounce, (b) the cosmological constant problem is reinterpreted, since accelerating phases can be mimicked by the change of geometry with the time scale, without invoking a slowly rolling scalar field, (c) the discreteness of geometry at Planckian scales can leave an observable imprint of logarithmic oscillations in cosmological spectra and (d) give rise to an alternative mechanism to inflation or (e) to a fully analytic model of cyclic mild inflation, where near scale invariance of the perturbation spectrum can be produced without strong acceleration. Various properties of the models and exact dynamical solutions are discussed. In particular, the multi-scale geometry with weighted derivatives is shown to be a Weyl integrable spacetime.

  18. Multi-Scale Change Detection Research of Remotely Sensed Big Data in CyberGIS

    NASA Astrophysics Data System (ADS)

    Xing, J.; Sieber, R.

    2015-12-01

    Big remotely sensed data, the heterogeneity of satellite platforms and file formats along with increasing volumes and velocities, offers new types of analyses. This makes big remotely sensed data a good candidate for CyberGIS, the aim of which is to enable knowledge discovery of big data in the cloud. We apply CyberGIS to feature-based multi-scale land use/cover change (LUCC) detection. There have been attempts to do multi-scale LUCC. However, studies were done with small data and could not consider the mismatch between multi-scale analysis and computational scale. They have yet to consider the possibilities for scalar research across numerous temporal and spatial scales afforded by big data, especially if we want to advance beyond pixel-based analysis and also reduce preprocessing requirements. We create a geospatial cyberinfrastructure (GCI) to handle multi-spatio-temporal scale change detection. We first clarify different meanings of scale in CyberGIS and LUCC to derive a feature scope layer in the GCI based on Stommel modelling. Our analysis layer contains a multi-scale segmentation-based method based on normalized cut image segmentation and wavelet-based image scaling algorithms. Our computer resource utilization layer uses Wang and Armstrong's (2009) method for mainly for memory, I/O and CPU time. Our case is urban-rural change detection in the Greater Montreal Area (5 time periods, 2006-2012, 100 virtual machines), 36,000km2 and varying from 0.6m to 38m resolution. We present a ground truthed accuracy assessment of a change matrix that is composed of 6 feature classes at 12 different spatio-temporal scales, and the performance of the change detection GCI for multi-scale LUCC study. The GCI allows us to extract and coordinate different types of changes by varying spatio-temporal scales from the big imagery datasets.

  19. Ecohydrological Linkages, Multi-scale Processes, Temporal Variability, and Drivers of Change in a Degraded Pinyon-Juniper Watershed: Implications for Erosion Modeling

    NASA Astrophysics Data System (ADS)

    Allen, C. D.

    2006-12-01

    In 1993 long-term research began on the runoff and erosion dynamics of a pinyon-juniper woodland hillslope at Bandelier National Monument in northern New Mexico (USA). In the 1.09 ha Frijolito watershed, erosion has been continuously studied at 3 spatial scales: 1 square meter, about 1000 square meters, and the entire watershed. This site is currently representative of degraded woodlands of pinyon (Pinus edulis) and one-seed juniper (Juniperus monosperma) in this region, exhibiting marked connectivity of exposed bare soil interspaces between tree canopy patches and obvious geomorphic signs of accelerated soil erosion (e.g., pedestalling, actively expanding rill networks). Ecological and land use histories show that this site has undergone a number of dramatic ecohydrological shifts since ca. C.E. 1850, transitioning from: 1) open ponderosa pine (Pinus ponderosa) overstory with limited pinyon-juniper component and substantial herbaceous understory that supported surface fires and constrained soil erosion, to; 2) ponderosa pine with reduced herbaceous cover due to livestock grazing after ca.1870, resulting in collapse of the surface fire regime and increased establishment of young pinyon and juniper trees, to; 3) mortality of all of the ponderosa pine during the extreme drought of the 1950s, leaving eroding pinyon-juniper woodland, to; 4) mortality of all mature pinyon at or above sapling size during the 2002-2003 drought, with juniper now the only dominant woody species. Detailed measurements since 1993 document high rates of soil erosion (> 2.75 Mg/ha/year on average at the watershed scale) that are rapidly stripping the local soils. Long-term observations are needed to distinguish short-term variability from longer term trends, as measurements of runoff and erosion show extreme variability at multiple time scales since 1993. The multi-scale erosion data from the Frijolito watershed reveal little dropoff in erosion rate (g/meter-squared) between the one meter

  20. Multi-scale modeling study of the source contributions to near-surface ozone and sulfur oxides levels over California during the ARCTAS-CARB period

    NASA Astrophysics Data System (ADS)

    Huang, M.; Carmichael, G. R.; Spak, S. N.; Adhikary, B.; Kulkarni, S.; Cheng, Y. F.; Wei, C.; Tang, Y.; D'Allura, A.; Wennberg, P. O.; Huey, G. L.; Dibb, J. E.; Jimenez, J. L.; Cubison, M. J.; Weinheimer, A. J.; Kaduwela, A.; Cai, C.; Wong, M.; Pierce, R. B.; Al-Saadi, J. A.; Streets, D. G.; Zhang, Q.

    2010-11-01

    Chronic ozone (O3) problems and the increasing sulfur oxides (SOx=SO2+SO4) ambient concentrations over South Coast (SC) and other areas of California (CA) are affected by both local emissions and long-range transport. In this paper, multi-scale tracer and full-chemistry simulations with the STEM atmospheric chemistry model are used to assess the contribution of local emission sources to SC O3 and evaluate the impacts of transported sulfur and local emissions on the SC sulfur budget during the ARCTAS-CARB experiment period in 2008. Sensitivity simulations quantify contributions of biogenic and fire emissions to SC O3 levels. California biogenic and fire emissions contribute 3-4 ppb to near-surface O3 over SC, with larger contributions to other regions in CA. Long-range transport from Asia is estimated to enhance surface SO4 over SC by ~0.5 μg/sm3, and the higher SOx levels (up to ~0.7 ppb of SO2 and ~6 μg/sm3 of SO4) observed above ~6 km did not affect surface air quality in the study region. Enhanced near-surface SOx levels over SC during the flight week were attributed mostly to local emissions. Two anthropogenic SOx emission inventories (EIs) from the California Air Resources Board (CARB) and the US Environmental Protection Agency (EPA) are compared and applied in 60 km and 12 km chemical transport simulations, and the results are compared with observations. The CARB EI shows improvements over the National Emission Inventory (NEI) by EPA, but generally underestimates surface SC SOx by about a factor of two. Maritime (mostly shipping) emissions contribute to the high SO2 levels over the ocean and on-shore, and fine SO4 over the downwind areas is impacted by maritime sources. Maritime emissions also modify the NOx-VOC limitations over coastal areas. These suggest an important role for shipping emission controls in reducing fine particle and O3 concentrations in SC.

  1. Multi-scale modeling study of the source contributions to near-surface ozone and sulfur oxides levels over California during the ARCTAS-CARB period

    NASA Astrophysics Data System (ADS)

    Huang, M.; Carmichael, G. R.; Spak, S. N.; Adhikary, B.; Kulkarni, S.; Cheng, Y.; Wei, C.; Tang, Y.; D'Allura, A.; Wennberg, P. O.; Huey, G. L.; Dibb, J. E.; Jimenez, J. L.; Cubison, M. J.; Weinheimer, A. J.; Kaduwela, A.; Cai, C.; Wong, M.; Pierce, R. Bradley; Al-Saadi, J. A.; Streets, D. G.; Zhang, Q.

    2011-04-01

    Chronic high surface ozone (O3) levels and the increasing sulfur oxides (SOx = SO2+SO4) ambient concentrations over South Coast (SC) and other areas of California (CA) are affected by both local emissions and long-range transport. In this paper, multi-scale tracer, full-chemistry and adjoint simulations using the STEM atmospheric chemistry model are conducted to assess the contribution of local emission sourcesto SC O3 and to evaluate the impacts of transported sulfur and local emissions on the SC sulfur budgetduring the ARCTAS-CARB experiment period in 2008. Sensitivity simulations quantify contributions of biogenic and fire emissions to SC O3 levels. California biogenic and fire emissions contribute 3-4 ppb to near-surface O3 over SC, with larger contributions to other regions in CA. During a long-range transport event from Asia starting from 22 June, high SOx levels (up to ~0.7 ppb of SO2 and ~1.3 ppb of SO4) is observed above ~6 km, but they did not affect CA surface air quality. The elevated SOx observed at 1-4 km is estimated to enhance surface SOx over SC by ~0.25 ppb (upper limit) on ~24 June. The near-surface SOx levels over SC during the flight week are attributed mostly to local emissions. Two anthropogenic SOx emission inventories (EIs) from the California Air Resources Board (CARB) and the US Environmental Protection Agency (EPA) are compared and applied in 60 km and 12 km chemical transport simulations, and the results are compared withobservations. The CARB EI shows improvements over the National Emission Inventory (NEI) by EPA, but generally underestimates surface SC SOx by about a factor of two. Adjoint sensitivity analysis indicated that SO2 levels at 00:00 UTC (17:00 local time) at six SC surface sites were influenced by previous day maritime emissions over the ocean, the terrestrial emissions over nearby urban areas, and by transported SO2 from the north through both terrestrial and maritime areas. Overall maritime emissions contribute 10-70% of

  2. Evaluation of the Models-3 Community Multi-scale Air Quality (CMAQ) modeling system with observations obtained during the TRACE-P experiment: Comparison of ozone and its related species

    NASA Astrophysics Data System (ADS)

    Zhang, Meigen; Uno, Itsushi; Zhang, Renjian; Han, Zhiwei; Wang, Zifa; Pu, Yifen

    The Models-3 Community Multi-scale Air Quality (CMAQ) modeling system with meteorological fields calculated by the Regional Atmospheric Modeling System (RAMS) was applied to East Asia to investigate the transport and photochemical transformation of tropospheric ozone during the Transport and Chemical Evolution over the Pacific (TRACE-P) field campaign. Modeled concentrations of hydroxyl radical, hydroperoxyl radical, nitric oxide, nitrogen dioxide, ethene, ethane, carbon monoxide, and ozone were compared with observations obtained onboard of two aircrafts in order to evaluate the model performance. Comparison indicates that the model reproduced the tempo-spatial distributions of ozone and its related chemical species reasonably well, and most model results were within a factor of 2 of the observations.

  3. Viscoelastic Model for Lung Parenchyma for Multi-Scale Modeling of Respiratory System Phase I: Hypo-Elastic Model for CFD Implementation

    SciTech Connect

    Freed, Alan D.; Einstein, Daniel R.

    2011-04-14

    An isotropic constitutive model for the parenchyma of lung has been derived from the theory of hypo-elasticity. The intent is to use it to represent the mechanical response of this soft tissue in sophisticated, computational, fluid-dynamic models of the lung. This demands that the continuum model be accurate, yet simple and effcient. An objective algorithm for its numeric integration is provided. The response of the model is determined for several boundary-value problems whose experiments are used for material characterization. The effective elastic, bulk, and shear moduli, and Poisson’s ratio, as tangent functions, are also derived. The model is characterized against published experimental data for lung. A bridge between this continuum model and a dodecahedral model of alveolar geometry is investigated, with preliminary findings being reported.

  4. A time for multi-scale modeling of anti-fibrotic therapies. Comment on "Towards a unified approach in the modeling of fibrosis: A review with research perspectives" by Martine Ben Amar and Carlo Bianca

    NASA Astrophysics Data System (ADS)

    Wu, Min

    2016-07-01

    The development of anti-fibrotic therapies in diversities of diseases becomes more and more urgent recently, such as in pulmonary, renal and liver fibrosis [1,2], as well as in malignant tumor growths [3]. As reviewed by Ben Amar and Bianca [4], various theoretical, experimental and in-silico models have been developed to understand the fibrosis process, where the implication on therapeutic strategies has also been frequently demonstrated (e.g., [5-7]). In [4], these models are analyzed and sorted according to their approaches, and in the end of [4], a unified multi-scale approach was proposed to understand fibrosis. While one of the major purposes of extensive modeling of fibrosis is to shed light on therapeutic strategies, the theoretical, experimental and in-silico studies of anti-fibrosis therapies should be conducted more intensively.

  5. The Adaptive Multi-scale Simulation Infrastructure

    SciTech Connect

    Tobin, William R.

    2015-09-01

    The Adaptive Multi-scale Simulation Infrastructure (AMSI) is a set of libraries and tools developed to support the development, implementation, and execution of general multimodel simulations. Using a minimal set of simulation meta-data AMSI allows for minimally intrusive work to adapt existent single-scale simulations for use in multi-scale simulations. Support for dynamic runtime operations such as single- and multi-scale adaptive properties is a key focus of AMSI. Particular focus has been spent on the development on scale-sensitive load balancing operations to allow single-scale simulations incorporated into a multi-scale simulation using AMSI to use standard load-balancing operations without affecting the integrity of the overall multi-scale simulation.

  6. Advanced modeling to accelerate the scale up of carbon capture technologies

    SciTech Connect

    Miller, David C.; Sun, XIN; Storlie, Curtis B.; Bhattacharyya, Debangsu

    2015-06-01

    In order to help meet the goals of the DOE carbon capture program, the Carbon Capture Simulation Initiative (CCSI) was launched in early 2011 to develop, demonstrate, and deploy advanced computational tools and validated multi-scale models to reduce the time required to develop and scale-up new carbon capture technologies. This article focuses on essential elements related to the development and validation of multi-scale models in order to help minimize risk and maximize learning as new technologies progress from pilot to demonstration scale.

  7. APPLICATION OF A NEW LAND-SURFACE, DRY DEPOSITION, AND PBL MODEL IN THE MODELS-3 COMMUNITY MULTI-SCALE AIR QUALITY (CMAQ) MODEL SYSTEM

    EPA Science Inventory

    Like most air quality modeling systems, CMAQ divides the treatment of meteorological and chemical/transport processes into separate models run sequentially. A potential drawback to this approach is that it creates the illusion that these processes are minimally interdependent an...

  8. Multi-scale analysis for environmental dispersion in wetland flow

    NASA Astrophysics Data System (ADS)

    Wu, Zi; Li, Z.; Chen, G. Q.

    2011-08-01

    Presented in this work is a multi-scale analysis for longitudinal evolution of contaminant concentration in a fully developed flow through a shallow wetland channel. An environmental dispersion model for the mean concentration is devised as an extension of Taylor's classical formulation by a multi-scale analysis. Corresponding environmental dispersivity is found identical to that determined by the method of concentration moments. For typical contaminant constituents of chemical oxygen demand, biochemical oxygen demand, total phosphorus, total nitrogen and heavy metal, the evolution of contaminant cloud is illustrated with the critical length and duration of the contaminant cloud with constituent concentration beyond some given environmental standard level.

  9. Bio-inspired homogeneous multi-scale place recognition.

    PubMed

    Chen, Zetao; Lowry, Stephanie; Jacobson, Adam; Hasselmo, Michael E; Milford, Michael

    2015-12-01

    Robotic mapping and localization systems typically operate at either one fixed spatial scale, or over two, combining a local metric map and a global topological map. In contrast, recent high profile discoveries in neuroscience have indicated that animals such as rodents navigate the world using multiple parallel maps, with each map encoding the world at a specific spatial scale. While a number of theoretical-only investigations have hypothesized several possible benefits of such a multi-scale mapping system, no one has comprehensively investigated the potential mapping and place recognition performance benefits for navigating robots in large real world environments, especially using more than two homogeneous map scales. In this paper we present a biologically-inspired multi-scale mapping system mimicking the rodent multi-scale map. Unlike hybrid metric-topological multi-scale robot mapping systems, this new system is homogeneous, distinguishable only by scale, like rodent neural maps. We present methods for training each network to learn and recognize places at a specific spatial scale, and techniques for combining the output from each of these parallel networks. This approach differs from traditional probabilistic robotic methods, where place recognition spatial specificity is passively driven by models of sensor uncertainty. Instead we intentionally create parallel learning systems that learn associations between sensory input and the environment at different spatial scales. We also conduct a systematic series of experiments and parameter studies that determine the effect on performance of using different neural map scaling ratios and different numbers of discrete map scales. The results demonstrate that a multi-scale approach universally improves place recognition performance and is capable of producing better than state of the art performance compared to existing robotic navigation algorithms. We analyze the results and discuss the implications with respect to

  10. Bio-inspired homogeneous multi-scale place recognition.

    PubMed

    Chen, Zetao; Lowry, Stephanie; Jacobson, Adam; Hasselmo, Michael E; Milford, Michael

    2015-12-01

    Robotic mapping and localization systems typically operate at either one fixed spatial scale, or over two, combining a local metric map and a global topological map. In contrast, recent high profile discoveries in neuroscience have indicated that animals such as rodents navigate the world using multiple parallel maps, with each map encoding the world at a specific spatial scale. While a number of theoretical-only investigations have hypothesized several possible benefits of such a multi-scale mapping system, no one has comprehensively investigated the potential mapping and place recognition performance benefits for navigating robots in large real world environments, especially using more than two homogeneous map scales. In this paper we present a biologically-inspired multi-scale mapping system mimicking the rodent multi-scale map. Unlike hybrid metric-topological multi-scale robot mapping systems, this new system is homogeneous, distinguishable only by scale, like rodent neural maps. We present methods for training each network to learn and recognize places at a specific spatial scale, and techniques for combining the output from each of these parallel networks. This approach differs from traditional probabilistic robotic methods, where place recognition spatial specificity is passively driven by models of sensor uncertainty. Instead we intentionally create parallel learning systems that learn associations between sensory input and the environment at different spatial scales. We also conduct a systematic series of experiments and parameter studies that determine the effect on performance of using different neural map scaling ratios and different numbers of discrete map scales. The results demonstrate that a multi-scale approach universally improves place recognition performance and is capable of producing better than state of the art performance compared to existing robotic navigation algorithms. We analyze the results and discuss the implications with respect to

  11. Multi-Scale Sizing of Lightweight Multifunctional Spacecraft Structural Components

    NASA Technical Reports Server (NTRS)

    Bednarcyk, Brett A.

    2005-01-01

    This document is the final report for the project entitled, "Multi-Scale Sizing of Lightweight Multifunctional Spacecraft Structural Components," funded under the NRA entitled "Cross-Enterprise Technology Development Program" issued by the NASA Office of Space Science in 2000. The project was funded in 2001, and spanned a four year period from March, 2001 to February, 2005. Through enhancements to and synthesis of unique, state of the art structural mechanics and micromechanics analysis software, a new multi-scale tool has been developed that enables design, analysis, and sizing of advance lightweight composite and smart materials and structures from the full vehicle, to the stiffened structure, to the micro (fiber and matrix) scales. The new software tool has broad, cross-cutting value to current and future NASA missions that will rely on advanced composite and smart materials and structures.

  12. Control of Thermo-Acoustics Instabilities: The Multi-Scale Extended Kalman Approach

    NASA Technical Reports Server (NTRS)

    Le, Dzu K.; DeLaat, John C.; Chang, Clarence T.

    2003-01-01

    "Multi-Scale Extended Kalman" (MSEK) is a novel model-based control approach recently found to be effective for suppressing combustion instabilities in gas turbines. A control law formulated in this approach for fuel modulation demonstrated steady suppression of a high-frequency combustion instability (less than 500Hz) in a liquid-fuel combustion test rig under engine-realistic conditions. To make-up for severe transport-delays on control effect, the MSEK controller combines a wavelet -like Multi-Scale analysis and an Extended Kalman Observer to predict the thermo-acoustic states of combustion pressure perturbations. The commanded fuel modulation is composed of a damper action based on the predicted states, and a tones suppression action based on the Multi-Scale estimation of thermal excitations and other transient disturbances. The controller performs automatic adjustments of the gain and phase of these actions to minimize the Time-Scale Averaged Variances of the pressures inside the combustion zone and upstream of the injector. The successful demonstration of Active Combustion Control with this MSEK controller completed an important NASA milestone for the current research in advanced combustion technologies.

  13. PERFORM 60 - Prediction of the effects of radiation for reactor pressure vessel and in-core materials using multi-scale modelling - 60 years foreseen plant lifetime

    NASA Astrophysics Data System (ADS)

    Leclercq, Sylvain; Lidbury, David; Van Dyck, Steven; Moinereau, Dominique; Alamo, Ana; Mazouzi, Abdou Al

    2010-11-01

    In nuclear power plants, materials may undergo degradation due to severe irradiation conditions that may limit their operational life. Utilities that operate these reactors need to quantify the ageing and the potential degradations of some essential structures of the power plant to ensure safe and reliable plant operation. So far, the material databases needed to take account of these degradations in the design and safe operation of installations mainly rely on long-term irradiation programs in test reactors as well as on mechanical or corrosion testing in specialized hot cells. Continuous progress in the physical understanding of the phenomena involved in irradiation damage and continuous progress in computer sciences have now made possible the development of multi-scale numerical tools able to simulate the effects of irradiation on materials microstructure. A first step towards this goal has been successfully reached through the development of the RPV-2 and Toughness Module numerical tools by the scientific community created around the FP6 PERFECT project. These tools allow to simulate irradiation effects on the constitutive behaviour of the reactor pressure vessel low alloy steel, and also on its failure properties. Relying on the existing PERFECT Roadmap, the 4 years Collaborative Project PERFORM 60 has mainly for objective to develop multi-scale tools aimed at predicting the combined effects of irradiation and corrosion on internals (austenitic stainless steels) and also to improve existing ones on RPV (bainitic steels). PERFORM 60 is based on two technical sub-projects: (i) RPV and (ii) internals. In addition to these technical sub-projects, the Users' Group and Training sub-project shall allow representatives of constructors, utilities, research organizations… from Europe, USA and Japan to receive the information and training to get their own appraisal on limits and potentialities of the developed tools. An important effort will also be made to teach young

  14. SENSITIVITY OF OZONE AND AEROSOL PREDICTIONS TO THE TRANSPORT ALGORITHMS IN THE MODELS-3 COMMUNITY MULTI-SCALE AIR QUALITY (CMAQ) MODELING SYSTEM

    EPA Science Inventory

    EPA's Models-3 CMAQ system is intended to provide a community modeling paradigm that allows continuous improvement of the one-atmosphere modeling capability in a unified fashion. CMAQ's modular design promotes incorporation of several sets of science process modules representing ...

  15. Metabolic Dynamics in Skeletal Muscle during Acute Reduction in Blood Flow and Oxygen Supply to Mitochondria: In-Silico Studies Using a Multi-Scale, Top-Down Integrated Model

    PubMed Central

    Dash, Ranjan K.; Li, Yanjun; Kim, Jaeyeon; Beard, Daniel A.; Saidel, Gerald M.; Cabrera, Marco E.

    2008-01-01

    Control mechanisms of cellular metabolism and energetics in skeletal muscle that may become evident in response to physiological stresses such as reduction in blood flow and oxygen supply to mitochondria can be quantitatively understood using a multi-scale computational model. The analysis of dynamic responses from such a model can provide insights into mechanisms of metabolic regulation that may not be evident from experimental studies. For the purpose, a physiologically-based, multi-scale computational model of skeletal muscle cellular metabolism and energetics was developed to describe dynamic responses of key chemical species and reaction fluxes to muscle ischemia. The model, which incorporates key transport and metabolic processes and subcellular compartmentalization, is based on dynamic mass balances of 30 chemical species in both capillary blood and tissue cells (cytosol and mitochondria) domains. The reaction fluxes in cytosol and mitochondria are expressed in terms of a general phenomenological Michaelis-Menten equation involving the compartmentalized energy controller ratios ATP/ADP and NADH/NAD+. The unknown transport and reaction parameters in the model are estimated simultaneously by minimizing the differences between available in vivo experimental data on muscle ischemia and corresponding model outputs in coupled with the resting linear flux balance constraints using a robust, nonlinear, constrained-based, reduced gradient optimization algorithm. With the optimal parameter values, the model is able to simulate dynamic responses to reduced blood flow and oxygen supply to mitochondria associated with muscle ischemia of several key metabolite concentrations and metabolic fluxes in the subcellular cytosolic and mitochondrial compartments, some that can be measured and others that can not be measured with the current experimental techniques. The model can be applied to test complex hypotheses involving dynamic regulation of cellular metabolism and

  16. [Multi-Scale Convergence of Cold-Land Process Representation in Land-Surface Models, Microwave Remote Sensing, and Field Observations

    NASA Technical Reports Server (NTRS)

    Shi, Jiancheng

    2005-01-01

    The cryosphere is a major component of the hydrosphere and interacts significantly with the global climate system, the geosphere, and the biosphere. Measurement of the amount of water stored in the snow pack and forecasting the rate of melt are thus essential for managing water supply and flood control systems. Snow hydrologists are confronted with the dual problems of estimating both the quantity of water held by seasonal snow packs and time of snow melt. Monitoring these snow parameters is essential for one of the objectives of the Earth Science Enterprise-understanding of the global hydrologic cycle. Measuring spatially distributed snow properties, such as snow water equivalence (SWE) and wetness, from space is a key component for improvement of our understanding of coupled atmosphere-surface processes. Through the GWEC project, we have significantly advanced our understandings and improved modeling capabilities of the microwave signatures in response to snow and underground properties.

  17. Multi-scale modeling of Puget Sound using an unstructured-grid coastal ocean model: from tide flats to estuaries and coastal waters

    SciTech Connect

    Yang, Zhaoqing; Khangaonkar, Tarang

    2010-11-19

    Water circulation in Puget Sound, a large complex estuary system in the Pacific Northwest coastal ocean of the United States, is governed by multiple spatially and temporally varying forcings from tides, atmosphere (wind, heating/cooling, precipitation/evaporation, pressure), and river inflows. In addition, the hydrodynamic response is affected strongly by geomorphic features, such as fjord-like bathymetry and complex shoreline features, resulting in many distinguishing characteristics in its main and sub-basins. To better understand the details of circulation features in Puget Sound and to assist with proposed nearshore restoration actions for improving water quality and the ecological health of Puget Sound, a high-resolution (around 50 m in estuaries and tide flats) hydrodynamic model for the entire Puget Sound was needed. Here, a threedimensional circulation model of Puget Sound using an unstructured-grid finite volume coastal ocean model is presented. The model was constructed with sufficient resolution in the nearshore region to address the complex coastline, multi-tidal channels, and tide flats. Model open boundaries were extended to the entrance of the Strait of Juan de Fuca and the northern end of the Strait of Georgia to account for the influences of ocean water intrusion from the Strait of Juan de Fuca and the Fraser River plume from the Strait of Georgia, respectively. Comparisons of model results, observed data, and associated error statistics for tidal elevation, velocity, temperature, and salinity indicate that the model is capable of simulating the general circulation patterns on the scale of a large estuarine system as well as detailed hydrodynamics in the nearshore tide flats. Tidal characteristics, temperature/salinity stratification, mean circulation, and river plumes in estuaries with tide flats are discussed.

  18. Innovation of Ozone Initial Concentration and Boundary Condition for Models-3 Community Multi-scale Air Quality (CMAQ) Modeling System Using Ozone Climatology and Its Impacts

    NASA Astrophysics Data System (ADS)

    He, S.; Vukovich, F. M.; Ching, J.; Gilliland, A.

    2002-05-01

    Models-3/CMAQ system is designed to provide a comprehensive and flexible modeling tool for states and other government agencies, and for scientific studies. The current setting of initial concentrations and boundary condition (ICBC) of air species for CMAQ system represents clean ambient condition in the eastern-half of the US, and as such. The ozone ICBC differed from observational values, significantly at upper troposphere. Because of the stratosphere-troposphere exchange, the upper troposphere may contain high concentrations of ozone (hundreds of ppbv). However the current ICBC artificially set ozone level as 70ppbv in upper troposphere throughout model domain. The large difference of standard ozone ICBC from realistic situation becomes considerable uncertainty source of CMAQ system. The purpose of this research is to improve ICBC setting for Models-3/CMAQ modeling system, and to assess the influence of introducing stratospheric ozone into troposphere on regional and urban air quality and on the tropospheric ozone budget. The approach taken is to perform a series of sensitivity studies on ICBC with CMAQ. The simulation covers the entire US with 108km grid resolution from July 2 to 12 of 1988. The domain divide in 34 layers vertically up to 40mbar. In addition to the base case with standard ICBC, ozone initial concentration and boundary condition are generated based on ozone climatology (Logan, 1999), which was derived from surface, satellite, and ozonesonde data across the globe. This new ICBC enables CMAQ model to study ozone cross-tropopause flux transporting to lower troposphere, and to analyze the impact of intercontinental ozone transport. The tropospheric ozone residue (TOR) data is used to compare with modeling tropospheric ozone budget for evaluation of CMAQ performance. Since ozone climatology was based on observation, the derived ozone ICBC are in better agreement with the ``real'' atmosphere than standard ICBC. CMAQ simulations with ozone climatology

  19. A multi-scale statistical study of twinning in magnesium

    NASA Astrophysics Data System (ADS)

    Tomé, C. N.; Beyerlein, I. J.; Wang, J.; McCabe, R. J.

    2011-03-01

    Hexagonal close packed (HCP) materials such as Mg, Zr, Ti, and Be are used in automotive, nuclear, aeronautic, and defense technologies. Understanding and controlling the formability of these materials is extremely relevant for these technologies. Such understanding requires an understanding of deformation twinning, an important deformation mechanism in HCP. Here we present a multi-scale modeling paradigm that passes information from the atomistic scale to the mesoscale represented by an individual grain in a polycrystalline metal. The single crystal model is, in turn, integrated into an Effective Medium model, which relates the behavior of all grains in the aggregate to the bulk response, such as stress-strain and texture evolution. This article focuses on application of the multi-scale model to HCP polycrystalline magnesium.

  20. Multi-Scale Simulation and Optimization of Lithium Battery Performance

    NASA Astrophysics Data System (ADS)

    Golmon, Stephanie L.

    The performance and degradation of lithium batteries strongly depends on electrochemical, mechanical, and thermal phenomena. While a large volume of work has focused on thermal management, mechanical phenomena relevant to battery design are not fully understood. Mechanical degradation of electrode particles has been experimentally linked to capacity fade and failure of batteries; an understanding of the interplay between mechanics and electrochemistry in the battery is necessary in order to improve the overall performance of the battery. A multi-scale model to simulate the coupled electrochemical and mechanical behavior of Li batteries has been developed, which models the porous electrode and separator regions of the battery. The porous electrode includes a liquid electrolyte and solid active materials. A multi-scale finite element approach is used to analyze the electrochemical and mechanical performance. The multi-scale model includes a macro- and micro-scale with analytical volume-averaging methods to relate the scales. The macro-scale model describes Li-ion transport through the electrolyte, electric potentials, and displacements throughout the battery. The micro-scale considers the surface kinetics and electrochemical and mechanical response of a single particle of active material evaluated locally within the cathode region. Both scales are non-linear and dependent on the other. The electrochemical and mechanical response of the battery are highly dependent on the porosity in the electrode, the active material particle size, and discharge rate. Balancing these parameters can improve the overall performance of the battery. A formal design optimization approach with multi-scale adjoint sensitivity analysis is developed to find optimal designs to improve the performance of the battery model. Optimal electrode designs are presented which maximize the capacity of the battery while mitigating stress levels during discharge over a range of discharge rates.

  1. Radiation Damage in Nuclear Fuel for Advanced Burner Reactors: Modeling and Experimental Validation

    SciTech Connect

    Jensen, Niels Gronbech; Asta, Mark; Ozolins, Nigel Browning'Vidvuds; de Walle, Axel van; Wolverton, Christopher

    2011-12-29

    The consortium has completed its existence and we are here highlighting work and accomplishments. As outlined in the proposal, the objective of the work was to advance the theoretical understanding of advanced nuclear fuel materials (oxides) toward a comprehensive modeling strategy that incorporates the different relevant scales involved in radiation damage in oxide fuels. Approaching this we set out to investigate and develop a set of directions: 1) Fission fragment and ion trajectory studies through advanced molecular dynamics methods that allow for statistical multi-scale simulations. This work also includes an investigation of appropriate interatomic force fields useful for the energetic multi-scale phenomena of high energy collisions; 2) Studies of defect and gas bubble formation through electronic structure and Monte Carlo simulations; and 3) an experimental component for the characterization of materials such that comparisons can be obtained between theory and experiment.

  2. Bridging the PSI Knowledge Gap: A Multi-Scale Approach

    SciTech Connect

    Wirth, Brian D.

    2015-01-08

    Plasma-surface interactions (PSI) pose an immense scientific hurdle in magnetic confinement fusion and our present understanding of PSI in confinement environments is highly inadequate; indeed, a recent Fusion Energy Sciences Advisory Committee report found that 4 out of the 5 top five fusion knowledge gaps were related to PSI. The time is appropriate to develop a concentrated and synergistic science effort that would expand, exploit and integrate the wealth of laboratory ion-beam and plasma research, as well as exciting new computational tools, towards the goal of bridging the PSI knowledge gap. This effort would broadly advance plasma and material sciences, while providing critical knowledge towards progress in fusion PSI. This project involves the development of a Science Center focused on a new approach to PSI science; an approach that both exploits access to state-of-the-art PSI experiments and modeling, as well as confinement devices. The organizing principle is to develop synergistic experimental and modeling tools that treat the truly coupled multi-scale aspect of the PSI issues in confinement devices. This is motivated by the simple observation that while typical lab experiments and models allow independent manipulation of controlling variables, the confinement PSI environment is essentially self-determined with few outside controls. This means that processes that may be treated independently in laboratory experiments, because they involve vastly different physical and time scales, will now affect one another in the confinement environment. Also, lab experiments cannot simultaneously match all exposure conditions found in confinement devices typically forcing a linear extrapolation of lab results. At the same time programmatic limitations prevent confinement experiments alone from answering many key PSI questions. The resolution to this problem is to usefully exploit access to PSI science in lab devices, while retooling our thinking from a linear and de

  3. A novel method of multi-scale simulation of macro-scale deformation and microstructure evolution on metal forming

    NASA Astrophysics Data System (ADS)

    Huang, Shiquan; Yi, Youping; Li, Pengchuan

    2011-05-01

    In recent years, multi-scale simulation technique of metal forming is gaining significant attention for prediction of the whole deformation process and microstructure evolution of product. The advances of numerical simulation at macro-scale level on metal forming are remarkable and the commercial FEM software, such as Deform2D/3D, has found a wide application in the fields of metal forming. However, the simulation method of multi-scale has little application due to the non-linearity of microstructure evolution during forming and the difficulty of modeling at the micro-scale level. This work deals with the modeling of microstructure evolution and a new method of multi-scale simulation in forging process. The aviation material 7050 aluminum alloy has been used as example for modeling of microstructure evolution. The corresponding thermal simulated experiment has been performed on Gleeble 1500 machine. The tested specimens have been analyzed for modeling of dislocation density, nucleation and growth of recrystallization(DRX). The source program using cellular automaton (CA) method has been developed to simulate the grain nucleation and growth, in which the change of grain topology structure caused by the metal deformation was considered. The physical fields at macro-scale level such as temperature field, stress and strain fields, which can be obtained by commercial software Deform 3D, are coupled with the deformed storage energy at micro-scale level by dislocation model to realize the multi-scale simulation. This method was explained by forging process simulation of the aircraft wheel hub forging. Coupled the results of Deform 3D with CA results, the forging deformation progress and the microstructure evolution at any point of forging could be simulated. For verifying the efficiency of simulation, experiments of aircraft wheel hub forging have been done in the laboratory and the comparison of simulation and experiment result has been discussed in details.

  4. Multi-scale interactions in Dictyostelium discoideum aggregation

    NASA Astrophysics Data System (ADS)

    Dixon, James A.; Kelty-Stephen, Damian G.

    2012-12-01

    Cellular aggregation is essential for a wide range of phenomena in developmental biology, and a crucial event in the life-cycle of Dictyostelium discoideum. The current manuscript presents an analysis of multi-scale interactions involved in D. discoideum aggregation and non-aggregation events. The multi-scale fractal dimensions of a sequence of microscope images were used to estimate changing structure at different spatial scales. Three regions showing aggregation and three showing non-aggregation were considered. The results showed that both aggregation and non-aggregation regions were strongly multi-fractal. Analyses of the over-time relationships among nine scales of the generalized dimension, D(q), were conducted using vector autoregression and vector error-correction models. Both types of regions showed evidence that across-scale interactions serve to maintain the equilibrium of the system. Aggregation and non-aggregation regions also showed different patterns of effects of individual scales on other scales. Specifically, aggregation regions showed greater effects of both the smallest and largest scales on the smaller scale structures. The results suggest that multi-scale interactions are responsible for maintaining and altering the cellular structures during aggregation.

  5. Collaborating for Multi-Scale Chemical Science

    SciTech Connect

    William H. Green

    2006-07-14

    Advanced model reduction methods were developed and integrated into the CMCS multiscale chemical science simulation software. The new technologies were used to simulate HCCI engines and burner flames with exceptional fidelity.

  6. Advanced Concept Modeling

    NASA Technical Reports Server (NTRS)

    Chaput, Armand; Johns, Zachary; Hodges, Todd; Selfridge, Justin; Bevirt, Joeben; Ahuja, Vivek

    2015-01-01

    Advanced Concepts Modeling software validation, analysis, and design. This was a National Institute of Aerospace contract with a lot of pieces. Efforts ranged from software development and validation for structures and aerodynamics, through flight control development, and aeropropulsive analysis, to UAV piloting services.

  7. Investigation of mechanism of bone regeneration in a porous biodegradable calcium phosphate (CaP) scaffold by a combination of a multi-scale agent-based model and experimental optimization/validation.

    PubMed

    Zhang, Le; Qiao, Minna; Gao, Hongjie; Hu, Bin; Tan, Hua; Zhou, Xiaobo; Li, Chang Ming

    2016-08-21

    Herein, we have developed a novel approach to investigate the mechanism of bone regeneration in a porous biodegradable calcium phosphate (CaP) scaffold by a combination of a multi-scale agent-based model, experimental optimization of key parameters and experimental data validation of the predictive power of the model. The advantages of this study are that the impact of mechanical stimulation on bone regeneration in a porous biodegradable CaP scaffold is considered, experimental design is used to investigate the optimal combination of growth factors loaded on the porous biodegradable CaP scaffold to promote bone regeneration and the training, testing and analysis of the model are carried out by using experimental data, a data-mining algorithm and related sensitivity analysis. The results reveal that mechanical stimulation has a great impact on bone regeneration in a porous biodegradable CaP scaffold and the optimal combination of growth factors that are encapsulated in nanospheres and loaded into porous biodegradable CaP scaffolds layer-by-layer can effectively promote bone regeneration. Furthermore, the model is robust and able to predict the development of bone regeneration under specified conditions.

  8. Investigation of mechanism of bone regeneration in a porous biodegradable calcium phosphate (CaP) scaffold by a combination of a multi-scale agent-based model and experimental optimization/validation

    NASA Astrophysics Data System (ADS)

    Zhang, Le; Qiao, Minna; Gao, Hongjie; Hu, Bin; Tan, Hua; Zhou, Xiaobo; Li, Chang Ming

    2016-08-01

    Herein, we have developed a novel approach to investigate the mechanism of bone regeneration in a porous biodegradable calcium phosphate (CaP) scaffold by a combination of a multi-scale agent-based model, experimental optimization of key parameters and experimental data validation of the predictive power of the model. The advantages of this study are that the impact of mechanical stimulation on bone regeneration in a porous biodegradable CaP scaffold is considered, experimental design is used to investigate the optimal combination of growth factors loaded on the porous biodegradable CaP scaffold to promote bone regeneration and the training, testing and analysis of the model are carried out by using experimental data, a data-mining algorithm and related sensitivity analysis. The results reveal that mechanical stimulation has a great impact on bone regeneration in a porous biodegradable CaP scaffold and the optimal combination of growth factors that are encapsulated in nanospheres and loaded into porous biodegradable CaP scaffolds layer-by-layer can effectively promote bone regeneration. Furthermore, the model is robust and able to predict the development of bone regeneration under specified conditions.

  9. Wyoming greater sage-grouse habitat prioritization: a collection of multi-scale seasonal models and geographic information systems land management tools

    USGS Publications Warehouse

    O'Donnell, Michael S.; Aldridge, Cameron L.; Doherty, Kevin E.; Fedy, Bradley C.

    2015-01-01

    We deliver all products described herein as online geographic information system data for visualization and downloading. We outline the data properties for each model and their data inputs, describe the process of selecting appropriate data products for multifarious applications, describe all data products and software, provide newly derived model composites, and discuss how land managers may use the models to inform future sage-grouse studies and potentially refine conservation efforts. The models, software tools, and associated opportunities for novel applications of these products should provide a suite of additional, but not exclusive, tools for assessing Wyoming Greater Sage-grouse habitats, which land managers, conservationists, and scientists can apply to myriad applications.

  10. Nanostructured particles from multi scale building blocks

    NASA Astrophysics Data System (ADS)

    Hampsey, J. Eric

    Nanotechnology has emerged as one of the most exciting new and developing fields in science today. New nanoscale materials and devices such as nanoparticles, nanocomposites, nanowires, and nanosensors could revolutionize the 21st century in the same way that the transistor and Internet led to the information age. One key component in developing these new technologies is to assemble individual atomic and molecular building blocks into larger structures with fundamentally new properties and functions. Nature is very efficient at assembling multi scale building blocks such as proteins, lipids, and minerals into nanostructured materials such as bone, teeth, diatoms, eggshells, seashells, cell membranes, and DNA. Surfactant and colloidal building block can also be assembled into different nanoscale materials and devices by utilizing hydrophobic/hydrophilic and other surface interactions. Using these concepts, this dissertation focuses on the syntheses and applications of nanostructured particles assembled from multi scale building blocks. Important factors in the synthesis of the particles include particle size, particle morphology, pore size and pore structure. Five different types of nanostructured particles assembled from different multi scale building blocks are demonstrated in this work: (1) Spherical metal/silica mesoporous particles with high surface areas and controllable pore sizes, pore structures, and metal content are synthesized from surfactant, silicate, and metal building blocks for catalytic applications; (2) Mesoporous hollow spheres with controllable pore sizes and pore structures are synthesized from surfactant, silica, and polystyrene building blocks; (3) Spherical mesoporous carbon particles with controllable pore sizes and pore structures are templated from silica particles assembled from silica and surfactant building blocks; (4) Spherical mesoporous, microporous, and bimodal carbon particles are synthesized from sucrose and silica building blocks

  11. Multi-Scale Approach for Predicting Fish Species Distributions across Coral Reef Seascapes

    PubMed Central

    Pittman, Simon J.; Brown, Kerry A.

    2011-01-01

    Two of the major limitations to effective management of coral reef ecosystems are a lack of information on the spatial distribution of marine species and a paucity of data on the interacting environmental variables that drive distributional patterns. Advances in marine remote sensing, together with the novel integration of landscape ecology and advanced niche modelling techniques provide an unprecedented opportunity to reliably model and map marine species distributions across many kilometres of coral reef ecosystems. We developed a multi-scale approach using three-dimensional seafloor morphology and across-shelf location to predict spatial distributions for five common Caribbean fish species. Seascape topography was quantified from high resolution bathymetry at five spatial scales (5–300 m radii) surrounding fish survey sites. Model performance and map accuracy was assessed for two high performing machine-learning algorithms: Boosted Regression Trees (BRT) and Maximum Entropy Species Distribution Modelling (MaxEnt). The three most important predictors were geographical location across the shelf, followed by a measure of topographic complexity. Predictor contribution differed among species, yet rarely changed across spatial scales. BRT provided ‘outstanding’ model predictions (AUC = >0.9) for three of five fish species. MaxEnt provided ‘outstanding’ model predictions for two of five species, with the remaining three models considered ‘excellent’ (AUC = 0.8–0.9). In contrast, MaxEnt spatial predictions were markedly more accurate (92% map accuracy) than BRT (68% map accuracy). We demonstrate that reliable spatial predictions for a range of key fish species can be achieved by modelling the interaction between the geographical location across the shelf and the topographic heterogeneity of seafloor structure. This multi-scale, analytic approach is an important new cost-effective tool to accurately delineate essential fish habitat and support

  12. Multiscale Modeling of the Deformation of Advanced Ferritic Steels for Generation IV Nuclear Energy

    SciTech Connect

    Nasr M. Ghoniem; Nick Kioussis

    2009-04-18

    The objective of this project is to use the multi-scale modeling of materials (MMM) approach to develop an improved understanding of the effects of neutron irradiation on the mechanical properties of high-temperature structural materials that are being developed or proposed for Gen IV applications. In particular, the research focuses on advanced ferritic/ martensitic steels to enable operation up to 650-700°C, compared to the current 550°C limit on high-temperature steels.

  13. Air quality forecast of PM10 in Beijing with Community Multi-scale Air Quality Modeling (CMAQ) system: emission and improvement

    NASA Astrophysics Data System (ADS)

    Wu, Q.; Xu, W.; Shi, A.; Li, Y.; Zhao, X.; Wang, Z.; Li, J.; Wang, L.

    2014-10-01

    The MM5-SMOKE-CMAQ model system, which was developed by the United States Environmental Protection Agency (US EPA) as the MODELS-3 system, has been used for daily air quality forecasts in the Beijing Municipal Environmental Monitoring Center (Beijing MEMC), as a part of the Ensemble air quality Modeling forecast System for Beijing (EMS-Beijing) since the 2008 Olympic Games. According to the daily forecast results for the entire duration of 2010, the model shows good performance in the PM10 forecast on most days but clearly underestimates PM10 concentration during some air pollution episodes. A typical air pollution episode from 11-20 January 2010 was chosen, in which the observed air pollution index of particulate matter (PM10-API) reached 180 while the forecast PM10-API was about 100. In this study, three numerical methods are used for model improvement: first, by enhancing the inner domain with 3 km resolution grids, and expanding the coverage from only Beijing to an area including Beijing and its surrounding cities; second, by adding more regional point source emissions located at Baoding, Landfang and Tangshan, to the south and east of Beijing; third, by updating the area source emissions, including the regional area source emissions in Baoding and Tangshan and the local village/town-level area source emissions in Beijing. The last two methods are combined as the updated emissions method. According to the model sensitivity testing results by the CMAQ model, the updated emissions method and expanded model domain method can both improve the model performance separately. But the expanded model domain method has better ability to capture the peak values of PM10 than the updated emissions method due to better reproduction of the pollution transport process in this episode. As a result, the hindcast results ("New(CMAQ)"), which are driven by the updated emissions in the expanded model domain, show a much better model performance in the national standard station

  14. A multi-scale model of dislocation plasticity in α-Fe: Incorporating temperature, strain rate and non-Schmid effects

    SciTech Connect

    Lim, H.; Hale, L. M.; Zimmerman, J. A.; Battaile, C. C.; Weinberger, C. R.

    2015-01-05

    In this study, we develop an atomistically informed crystal plasticity finite element (CP-FE) model for body-centered-cubic (BCC) α-Fe that incorporates non-Schmid stress dependent slip with temperature and strain rate effects. Based on recent insights obtained from atomistic simulations, we propose a new constitutive model that combines a generalized non-Schmid yield law with aspects from a line tension (LT) model for describing activation enthalpy required for the motion of dislocation kinks. Atomistic calculations are conducted to quantify the non-Schmid effects while both experimental data and atomistic simulations are used to assess the temperature and strain rate effects. The parameterized constitutive equation is implemented into a BCC CP-FE model to simulate plastic deformation of single and polycrystalline Fe which is compared with experimental data from the literature. This direct comparison demonstrates that the atomistically informed model accurately captures the effects of crystal orientation, temperature and strain rate on the flow behavior of siangle crystal Fe. Furthermore, our proposed CP-FE model exhibits temperature and strain rate dependent flow and yield surfaces in polycrystalline Fe that deviate from conventional CP-FE models based on Schmid's law.

  15. A multi-scale model of dislocation plasticity in α-Fe: Incorporating temperature, strain rate and non-Schmid effects

    DOE PAGES

    Lim, H.; Hale, L. M.; Zimmerman, J. A.; Battaile, C. C.; Weinberger, C. R.

    2015-01-05

    In this study, we develop an atomistically informed crystal plasticity finite element (CP-FE) model for body-centered-cubic (BCC) α-Fe that incorporates non-Schmid stress dependent slip with temperature and strain rate effects. Based on recent insights obtained from atomistic simulations, we propose a new constitutive model that combines a generalized non-Schmid yield law with aspects from a line tension (LT) model for describing activation enthalpy required for the motion of dislocation kinks. Atomistic calculations are conducted to quantify the non-Schmid effects while both experimental data and atomistic simulations are used to assess the temperature and strain rate effects. The parameterized constitutive equationmore » is implemented into a BCC CP-FE model to simulate plastic deformation of single and polycrystalline Fe which is compared with experimental data from the literature. This direct comparison demonstrates that the atomistically informed model accurately captures the effects of crystal orientation, temperature and strain rate on the flow behavior of siangle crystal Fe. Furthermore, our proposed CP-FE model exhibits temperature and strain rate dependent flow and yield surfaces in polycrystalline Fe that deviate from conventional CP-FE models based on Schmid's law.« less

  16. Multi-Scale Soil Moisture Monitoring and Modeling at ARS Watersheds for NASA's Soil Moisture Active Passive (SMAP) Calibration/Validation Mission

    NASA Astrophysics Data System (ADS)

    Coopersmith, E. J.; Cosh, M. H.

    2014-12-01

    NASA's SMAP satellite, launched in November of 2014, produces estimates of average volumetric soil moisture at 3, 9, and 36-kilometer scales. The calibration and validation process of these estimates requires the generation of an identically-scaled soil moisture product from existing in-situ networks. This can be achieved via the integration of NLDAS precipitation data to perform calibration of models at each ­in-situ gauge. In turn, these models and the gauges' volumetric estimations are used to generate soil moisture estimates at a 500m scale throughout a given test watershed by leveraging, at each location, the gauge-calibrated models deemed most appropriate in terms of proximity, calibration efficacy, soil-textural similarity, and topography. Four ARS watersheds, located in Iowa, Oklahoma, Georgia, and Arizona are employed to demonstrate the utility of this approach. The South Fork watershed in Iowa represents the simplest case - the soil textures and topography are relative constants and the variability of soil moisture is simply tied to the spatial variability of precipitation. The Little Washita watershed in Oklahoma adds soil textural variability (but remains topographically simple), while the Little River watershed in Georgia incorporates topographic classification. Finally, the Walnut Gulch watershed in Arizona adds a dense precipitation network to be employed for even finer-scale modeling estimates. Results suggest RMSE values at or below the 4% volumetric standard adopted for the SMAP mission are attainable over the desired spatial scales via this integration of modeling efforts and existing in-situ networks.

  17. Molecular-dynamics simulation of amphiphilic bilayer membranes and wormlike micelles: a multi-scale modelling approach to the design of viscoelastic surfactant solutions.

    PubMed

    Boek, E S; Den Otter, W K; Briels, W J; Iakovlev, D

    2004-08-15

    Bilayer membranes and wormlike micelles have been studied using molecular-dynamics simulations. The structure of the worm is analysed in terms of radial density distribution functions, and mechanical properties such as the elastic modulus are calculated. From an analysis of the fluctuation spectra of the tensionless states, we have calculated bending rigidities. Micelles consisting of coarse-grained (CG) model surfactants are studied in order to map the properties of the atomistic micelle. We optimize the CG model with respect to the structure factor of the atomistic micelle. The mechanical properties thus obtained will be used as input for a mesoscopic model of wormlike micelles where the persistence length is the smallest length-scale.

  18. The air quality forecast of PM10 in Beijing with Community Multi-scale Air Quality Modeling (CMAQ) system: emission and improvement

    NASA Astrophysics Data System (ADS)

    Wu, Q.; Xu, W.; Shi, A.; Li, Y.; Zhao, X.; Wang, Z.; Li, J.; Wang, L.

    2014-05-01

    The MM5-SMOKE-CMAQ model system, which was developed by the United States Environmental Protection Agency (US EPA) as the Models-3 system, has been used for daily air quality forecasts in the Beijing Municipal Environmental Monitoring Center (Beijing MEMC), as a part of the Ensemble Air Quality Forecast System for Beijing (EMS-Beijing) since the Olympic Games 2008. According to the daily forecast results for the entire duration of 2010, the model shows good model performances in the PM10 forecast on most days but clearly underestimates some air pollution episodes. A typical air pollution episode from 11-20 January 2010 was chosen, where the observed air pollution index of particulate matter (PM10-API) reached to 180 while the forecast's PM10-API was about 100. In this study, three numerical methods are used for model improvement: first, enhance the inner domain with 3 km resolution grids: the coverage is expanded from only Beijing to the area including Beijing and its surrounding cities; second, add more regional point source emissions located at Baoding, Landfang and Tangshan, which is to the south and east of Beijing; third, update the area source emissions, which includes the regional area source emissions in Baoding and Tangshan and the local village-town level area source emissions in Beijing. As a result, the hindcast shows a much better model performance in the national standard station-averaged PM10-API, whereas the daily hindcast PM10-API reaches 180 and is much closer to the observation and has a correlation coefficient of 0.93. The correlation coefficient of the PM10-API in all Beijing MEMC stations between the hindcast and observation is 0.82, obviously higher than the forecast's 0.54, and the FAC2 increases from 56% in the forecast to 84% in the hindcast, while the NMSE decreases from 0.886 to 0.196. The hindcast also has better model performance in PM10 hourly concentrations during the typical air pollution episode, the correlation coefficient

  19. Multi-scales and multi-satellites estimates of evapotranspiration with a residual energy balance model in the Muzza agricultural district in Northern Italy

    NASA Astrophysics Data System (ADS)

    Corbari, C.; Bissolati, M.; Mancini, M.

    2015-05-01

    Evapotranspiration estimates were performed with a residual energy balance model (REB) over an agricultural area using remote sensing data. REB uses land surface temperature (LST) as main input parameter so that energy fluxes were computed instantaneously at the time of data acquisition. Data from MODIS and SEVIRI sensors were used and downscaling techniques were implemented to improve their spatial resolutions. Energy fluxes at the original spatial resolutions (1000 m for MODIS and 5000 m for SEVIRI) as well as at the downscaled resolutions (250 m for MODIS and 1000 m for SEVIRI) were calculated with the REB model. Ground eddy covariance data and remote sensing information from the Muzza agricultural irrigation district in Italy from 2010 to 2012 gave the opportunity to validate and compare spatially distributed energy fluxes. The model outputs matched quite well ground observations when ground LST data were used, while differences increased when MODIS and SEVIRI LST were used. The spatial analysis revealed significant differences between the two sensors both in term of LST (around 2.8 °C) and of latent heat fluxes with values (around 100 W m-2).

  20. Estimating environmental conditions affecting protozoal pathogen removal in surface water wetland systems using a multi-scale, model-based approach.

    PubMed

    Daniels, Miles E; Hogan, Jennifer; Smith, Woutrina A; Oates, Stori C; Miller, Melissa A; Hardin, Dane; Shapiro, Karen; Los Huertos, Marc; Conrad, Patricia A; Dominik, Clare; Watson, Fred G R

    2014-09-15

    Cryptosporidium parvum, Giardia lamblia, and Toxoplasma gondii are waterborne protozoal pathogens distributed worldwide and empirical evidence suggests that wetlands reduce the concentrations of these pathogens under certain environmental conditions. The goal of this study was to evaluate how protozoal removal in surface water is affected by the water temperature, turbidity, salinity, and vegetation cover of wetlands in the Monterey Bay region of California. To examine how protozoal removal was affected by these environmental factors, we conducted observational experiments at three primary spatial scales: settling columns, recirculating wetland mesocosm tanks, and an experimental research wetland (Molera Wetland). Simultaneously, we developed a protozoal transport model for surface water to simulate the settling columns, the mesocosm tanks, and the Molera Wetland. With a high degree of uncertainty expected in the model predictions and field observations, we developed the model within a Bayesian statistical framework. We found protozoal removal increased when water flowed through vegetation, and with higher levels of turbidity, salinity, and temperature. Protozoal removal in surface water was maximized (~0.1 hour(-1)) when flowing through emergent vegetation at 2% cover, and with a vegetation contact time of ~30 minutes compared to the effects of temperature, salinity, and turbidity. Our studies revealed that an increase in vegetated wetland area, with water moving through vegetation, would likely improve regional water quality through the reduction of fecal protozoal pathogen loads.

  1. Multi-scale harmonic model for solar and climate cyclical variation throughout the Holocene based on Jupiter-Saturn tidal frequencies plus the 11-year solar dynamo cycle

    NASA Astrophysics Data System (ADS)

    Scafetta, Nicola

    2012-05-01

    The Schwabe frequency band of the Zurich sunspot record since 1749 is found to be made of three major cycles with periods of about 9.98, 10.9 and 11.86 years. The side frequencies appear to be closely related to the spring tidal period of Jupiter and Saturn (range between 9.5 and 10.5 years, and median 9.93 years) and to the tidal sidereal period of Jupiter (about 11.86 years). The central cycle may be associated to a quasi-11-year solar dynamo cycle that appears to be approximately synchronized to the average of the two planetary frequencies. A simplified harmonic constituent model based on the above two planetary tidal frequencies and on the exact dates of Jupiter and Saturn planetary tidal phases, plus a theoretically deduced 10.87-year central cycle reveals complex quasi-periodic interference/beat patterns. The major beat periods occur at about 115, 61 and 130 years, plus a quasi-millennial large beat cycle around 983 years. We show that equivalent synchronized cycles are found in cosmogenic records used to reconstruct solar activity and in proxy climate records throughout the Holocene (last 12,000 years) up to now. The quasi-secular beat oscillations hindcast reasonably well the known prolonged periods of low solar activity during the last millennium such as the Oort, Wolf, Spörer, Maunder and Dalton minima, as well as the 17 115-year long oscillations found in a detailed temperature reconstruction of the Northern Hemisphere covering the last 2000 years. The millennial three-frequency beat cycle hindcasts equivalent solar and climate cycles for 12,000 years. Finally, the harmonic model herein proposed reconstructs the prolonged solar minima that occurred during 1900-1920 and 1960-1980 and the secular solar maxima around 1870-1890, 1940-1950 and 1995-2005 and a secular upward trending during the 20th century: this modulated trending agrees well with some solar proxy model, with the ACRIM TSI satellite composite and with the global surface temperature

  2. Unveiling the factors shaping the distribution of widely distributed alpine vertebrates, using multi-scale ecological niche modelling of the bat Plecotus macrobullaris.

    PubMed

    Alberdi, Antton; Aizpurua, Ostaizka; Aihartza, Joxerra; Garin, Inazio

    2014-01-01

    Several alpine vertebrates share a distribution pattern that extends across the South-western Palearctic but is limited to the main mountain massifs. Although they are usually regarded as cold-adapted species, the range of many alpine vertebrates also includes relatively warm areas, suggesting that factors beyond climatic conditions may be driving their distribution. In this work we first recognize the species belonging to the mentioned biogeographic group and, based on the environmental niche analysis of Plecotus macrobullaris, we identify and characterize the environmental factors constraining their ranges. Distribution overlap analysis of 504 European vertebrates was done using the Sorensen Similarity Index, and we identified four birds and one mammal that share the distribution with P. macrobullaris. We generated 135 environmental niche models including different variable combinations and regularization values for P. macrobullaris at two different scales and resolutions. After selecting the best models, we observed that topographic variables outperformed climatic predictors, and the abruptness of the landscape showed better predictive ability than elevation. The best explanatory climatic variable was mean summer temperature, which showed that P. macrobullaris is able to cope with mean temperature ranges spanning up to 16°C. The models showed that the distribution of P. macrobullaris is mainly shaped by topographic factors that provide rock-abundant and open-space habitats rather than climatic determinants, and that the species is not a cold-adapted, but rather a cold-tolerant eurithermic organism. P. macrobullaris shares its distribution pattern as well as several ecological features with five other alpine vertebrates, suggesting that the conclusions obtained from this study might be extensible to them. We concluded that rock-dwelling and open-space foraging vertebrates with broad temperature tolerance are the best candidates to show wide alpine distribution

  3. Ocean deep convection in the Mediterranean sea: 2012-2013 case study in the Gulf of Lions, from observations to multi-scale modelling.

    NASA Astrophysics Data System (ADS)

    Waldman, Robin; Somot, Samuel; Herrmann, Marine; Sevault, Florence; Caniaux, Guy; Giordani, Hervé; Testor, Pierre; Estournel, Claude

    2015-04-01

    Ocean deep convection is a major process of interaction between surface and deep ocean, it indeed plays a major role in ocean heat and CO2 uptake in a warming climate, sea level rise and nutrient storage for marine biology. In this study, ocean deep convection is investigated in the Gulf of Lions, the main deep water formation (DWF) site in the Western Mediterranean sea. Recent observations in the frame of MOOSE, HyMeX and Mermex programmes allow for a thorough analysis of 2012-2013 convective year. The Mediterranean sea model NEMOMED12 ( 6km resolution) with its grid refinement ( 2km) is used as a numerical tool to characterize and understand ocean deep convection in 2012-2013. The model is initialized on august 1st 2012 using an ensemble of gridded reanalyses based on in situ observations (MOOSE 2012 ship cruise). The atmospheric forcing ALADIN-Climate is a dynamical downscaling of the ERA-INTERIM reanalysis at 12km and 3hr resolution over the 2012-2013 period. Near-Atlantic ocean conditions are damped towards ORAS4 reanalysis and river and Black Sea freshwater inflows are prescribed from climatologies. An assessment of large-scale convection is done for 2012-2013 year in NEMOMED12 and observations, allowing for a characterization of its chronology, intensity, location as well as the hydrology of the main water masses involved. This study addresses the respective impacts of atmospheric forcing, ocean preconditionning and mesoscale resolution to deep convection.

  4. Effect of global cardiac ischemia on human ventricular fibrillation: insights from a multi-scale mechanistic model of the human heart.

    PubMed

    Kazbanov, Ivan V; Clayton, Richard H; Nash, Martyn P; Bradley, Chris P; Paterson, David J; Hayward, Martin P; Taggart, Peter; Panfilov, Alexander V

    2014-11-01

    Acute regional ischemia in the heart can lead to cardiac arrhythmias such as ventricular fibrillation (VF), which in turn compromise cardiac output and result in secondary global cardiac ischemia. The secondary ischemia may influence the underlying arrhythmia mechanism. A recent clinical study documents the effect of global cardiac ischaemia on the mechanisms of VF. During 150 seconds of global ischemia the dominant frequency of activation decreased, while after reperfusion it increased rapidly. At the same time the complexity of epicardial excitation, measured as the number of epicardical phase singularity points, remained approximately constant during ischemia. Here we perform numerical studies based on these clinical data and propose explanations for the observed dynamics of the period and complexity of activation patterns. In particular, we study the effects on ischemia in pseudo-1D and 2D cardiac tissue models as well as in an anatomically accurate model of human heart ventricles. We demonstrate that the fall of dominant frequency in VF during secondary ischemia can be explained by an increase in extracellular potassium, while the increase during reperfusion is consistent with washout of potassium and continued activation of the ATP-dependent potassium channels. We also suggest that memory effects are responsible for the observed complexity dynamics. In addition, we present unpublished clinical results of individual patient recordings and propose a way of estimating extracellular potassium and activation of ATP-dependent potassium channels from these measurements. PMID:25375999

  5. Influence of the "surface effect" on the segregation parameters of S in Fe(100): A multi-scale modelling and Auger Electron Spectroscopy study

    NASA Astrophysics Data System (ADS)

    Barnard, P. E.; Terblans, J. J.; Swart, H. C.

    2015-12-01

    The article takes a new look at the process of atomic segregation by considering the influence of surface relaxation on the segregation parameters; the activation energy (Q), segregation energy (ΔG), interaction parameter (Ω) and the pre-exponential factor (D0). Computational modelling, namely Density Functional Theory (DFT) and the Modified Darken Model (MDM) in conjunction with Auger Electron Spectroscopy (AES) was utilized to study the variation of the segregation parameters for S in the surface region of Fe(100). Results indicate a variation in each of the segregation parameters as a function of the atomic layer under consideration. Values of the segregation parameters varied more dramatically as the surface layer is approached, with atomic layer 2 having the largest deviations in comparison to the bulk values. This atomic layer had the highest Q value and formed the rate limiting step for the segregation of S towards the Fe(100) surface. It was found that the segregation process is influenced by two sets of segregation parameters, those of the surface region formed by atomic layer 2, and those in the bulk material. This article is the first to conduct a full scale investigation on the influence of surface relaxation on segregation and labelled it the "surface effect".

  6. Multi-scale computation methods: Their applications in lithium-ion battery research and development

    NASA Astrophysics Data System (ADS)

    Siqi, Shi; Jian, Gao; Yue, Liu; Yan, Zhao; Qu, Wu; Wangwei, Ju; Chuying, Ouyang; Ruijuan, Xiao

    2016-01-01

    Based upon advances in theoretical algorithms, modeling and simulations, and computer technologies, the rational design of materials, cells, devices, and packs in the field of lithium-ion batteries is being realized incrementally and will at some point trigger a paradigm revolution by combining calculations and experiments linked by a big shared database, enabling accelerated development of the whole industrial chain. Theory and multi-scale modeling and simulation, as supplements to experimental efforts, can help greatly to close some of the current experimental and technological gaps, as well as predict path-independent properties and help to fundamentally understand path-independent performance in multiple spatial and temporal scales. Project supported by the National Natural Science Foundation of China (Grant Nos. 51372228 and 11234013), the National High Technology Research and Development Program of China (Grant No. 2015AA034201), and Shanghai Pujiang Program, China (Grant No. 14PJ1403900).

  7. Goal-oriented robot navigation learning using a multi-scale space representation.

    PubMed

    Llofriu, M; Tejera, G; Contreras, M; Pelc, T; Fellous, J M; Weitzenfeld, A

    2015-12-01

    There has been extensive research in recent years on the multi-scale nature of hippocampal place cells and entorhinal grid cells encoding which led to many speculations on their role in spatial cognition. In this paper we focus on the multi-scale nature of place cells and how they contribute to faster learning during goal-oriented navigation when compared to a spatial cognition system composed of single scale place cells. The task consists of a circular arena with a fixed goal location, in which a robot is trained to find the shortest path to the goal after a number of learning trials. Synaptic connections are modified using a reinforcement learning paradigm adapted to the place cells multi-scale architecture. The model is evaluated in both simulation and physical robots. We find that larger scale and combined multi-scale representations favor goal-oriented navigation task learning.

  8. Change detection based on integration of multi-scale mixed-resolution information

    NASA Astrophysics Data System (ADS)

    Wei, Li; Wang, Cheng; Wen, Chenglu

    2016-03-01

    In this paper, a new method of unsupervised change detection is proposed by modeling multi-scale change detector based on local mixed information and we present a method of automated threshold. A theoretical analysis is presented to demonstrate that more comprehensive information is taken into account by the integration of multi-scale information. The ROC curves show that change detector based on multi-scale mixed information(MSM) is more effective than based on mixed information(MIX). Experiments on artificial and real-world datasets indicate that the multi-scale change detection of mixed information can eliminate the pseudo-change part of the area. Therefore, the proposed algorithm MSM is an effective method for the application of change detection.

  9. Multi-scale study of condensation in water jets using ellipsoidal-statistical Bhatnagar-Gross-Krook and molecular dynamics modeling.

    PubMed

    Li, Zheng; Borner, Arnaud; Levin, Deborah A

    2014-06-14

    Homogeneous water condensation and ice formation in supersonic expansions to vacuum for stagnation pressures from 12 to 1000 mbar are studied using the particle-based Ellipsoidal-Statistical Bhatnagar-Gross-Krook (ES-BGK) method. We find that when condensation starts to occur, at a stagnation pressure of 96 mbar, the increase in the degree of condensation causes an increase in the rotational temperature due to the latent heat of vaporization. The simulated rotational temperature profiles along the plume expansion agree well with measurements confirming the kinetic homogeneous condensation models and the method of simulation. Comparisons of the simulated gas and cluster number densities, cluster size for different stagnation pressures along the plume centerline were made and it is found that the cluster size increase linearly with respect to stagnation pressure, consistent with classical nucleation theory. The sensitivity of our results to cluster nucleation model and latent heat values based on bulk water, specific cluster size, or bulk ice are examined. In particular, the ES-BGK simulations are found to be too coarse-grained to provide information on the phase or structure of the clusters formed. For this reason, molecular dynamics simulations of water condensation in a one-dimensional free expansion to simulate the conditions in the core of a plume are performed. We find that the internal structure of the clusters formed depends on the stagnation temperature. A larger cluster of average size 21 was tracked down the expansion, and a calculation of its average internal temperature as well as a comparison of its radial distribution functions (RDFs) with values measured for solid amorphous ice clusters lead us to conclude that this cluster is in a solid-like rather than liquid form. In another molecular-dynamics simulation at a much lower stagnation temperature, a larger cluster of size 324 and internal temperature 200 K was extracted from an expansion plume and

  10. Multi-scale study of condensation in water jets using ellipsoidal-statistical Bhatnagar-Gross-Krook and molecular dynamics modeling.

    PubMed

    Li, Zheng; Borner, Arnaud; Levin, Deborah A

    2014-06-14

    Homogeneous water condensation and ice formation in supersonic expansions to vacuum for stagnation pressures from 12 to 1000 mbar are studied using the particle-based Ellipsoidal-Statistical Bhatnagar-Gross-Krook (ES-BGK) method. We find that when condensation starts to occur, at a stagnation pressure of 96 mbar, the increase in the degree of condensation causes an increase in the rotational temperature due to the latent heat of vaporization. The simulated rotational temperature profiles along the plume expansion agree well with measurements confirming the kinetic homogeneous condensation models and the method of simulation. Comparisons of the simulated gas and cluster number densities, cluster size for different stagnation pressures along the plume centerline were made and it is found that the cluster size increase linearly with respect to stagnation pressure, consistent with classical nucleation theory. The sensitivity of our results to cluster nucleation model and latent heat values based on bulk water, specific cluster size, or bulk ice are examined. In particular, the ES-BGK simulations are found to be too coarse-grained to provide information on the phase or structure of the clusters formed. For this reason, molecular dynamics simulations of water condensation in a one-dimensional free expansion to simulate the conditions in the core of a plume are performed. We find that the internal structure of the clusters formed depends on the stagnation temperature. A larger cluster of average size 21 was tracked down the expansion, and a calculation of its average internal temperature as well as a comparison of its radial distribution functions (RDFs) with values measured for solid amorphous ice clusters lead us to conclude that this cluster is in a solid-like rather than liquid form. In another molecular-dynamics simulation at a much lower stagnation temperature, a larger cluster of size 324 and internal temperature 200 K was extracted from an expansion plume and

  11. The brain's code and its canonical computational motifs. From sensory cortex to the default mode network: A multi-scale model of brain function in health and disease.

    PubMed

    Turkheimer, Federico E; Leech, Robert; Expert, Paul; Lord, Louis-David; Vernon, Anthony C

    2015-08-01

    A variety of anatomical and physiological evidence suggests that the brain performs computations using motifs that are repeated across species, brain areas, and modalities. The computational architecture of cortex, for example, is very similar from one area to another and the types, arrangements, and connections of cortical neurons are highly stereotyped. This supports the idea that each cortical area conducts calculations using similarly structured neuronal modules: what we term canonical computational motifs. In addition, the remarkable self-similarity of the brain observables at the micro-, meso- and macro-scale further suggests that these motifs are repeated at increasing spatial and temporal scales supporting brain activity from primary motor and sensory processing to higher-level behaviour and cognition. Here, we briefly review the biological bases of canonical brain circuits and the role of inhibitory interneurons in these computational elements. We then elucidate how canonical computational motifs can be repeated across spatial and temporal scales to build a multiplexing information system able to encode and transmit information of increasing complexity. We point to the similarities between the patterns of activation observed in primary sensory cortices by use of electrophysiology and those observed in large scale networks measured with fMRI. We then employ the canonical model of brain function to unify seemingly disparate evidence on the pathophysiology of schizophrenia in a single explanatory framework. We hypothesise that such a framework may also be extended to cover multiple brain disorders which are grounded in dysfunction of GABA interneurons and/or these computational motifs.

  12. Understanding the complexity of the Lévy-walk nature of human mobility with a multi-scale cost∕benefit model.

    PubMed

    Scafetta, Nicola

    2011-12-01

    Probability distributions of human displacements have been fit with exponentially truncated Lévy flights or fat tailed Pareto inverse power law probability distributions. Thus, people usually stay within a given location (for example, the city of residence), but with a non-vanishing frequency they visit nearby or far locations too. Herein, we show that an important empirical distribution of human displacements (range: from 1 to 1000 km) can be well fit by three consecutive Pareto distributions with simple integer exponents equal to 1, 2, and (>) 3. These three exponents correspond to three displacement range zones of about 1 km ≲Δr≲10 km, 10 km ≲Δr≲300 km, and 300 km ≲Δr≲1000 km, respectively. These three zones can be geographically and physically well determined as displacements within a city, visits to nearby cities that may occur within just one-day trips, and visit to far locations that may require multi-days trips. The incremental integer values of the three exponents can be easily explained with a three-scale mobility cost∕benefit model for human displacements based on simple geometrical constrains. Essentially, people would divide the space into three major regions (close, medium, and far distances) and would assume that the travel benefits are randomly∕uniformly distributed mostly only within specific urban-like areas. The three displacement distribution zones appear to be characterized by an integer (1, 2, or >3) inverse power exponent because of the specific number (1, 2, or >3) of cost mechanisms (each of which is proportional to the displacement length). The distributions in the first two zones would be associated to Pareto distributions with exponent β = 1 and β = 2 because of simple geometrical statistical considerations due to the a priori assumption that most benefits are searched in the urban area of the city of residence or in the urban area of specific nearby cities. We also show, by using independent records of

  13. Understanding the complexity of the Lévy-walk nature of human mobility with a multi-scale cost∕benefit model.

    PubMed

    Scafetta, Nicola

    2011-12-01

    Probability distributions of human displacements have been fit with exponentially truncated Lévy flights or fat tailed Pareto inverse power law probability distributions. Thus, people usually stay within a given location (for example, the city of residence), but with a non-vanishing frequency they visit nearby or far locations too. Herein, we show that an important empirical distribution of human displacements (range: from 1 to 1000 km) can be well fit by three consecutive Pareto distributions with simple integer exponents equal to 1, 2, and (>) 3. These three exponents correspond to three displacement range zones of about 1 km ≲Δr≲10 km, 10 km ≲Δr≲300 km, and 300 km ≲Δr≲1000 km, respectively. These three zones can be geographically and physically well determined as displacements within a city, visits to nearby cities that may occur within just one-day trips, and visit to far locations that may require multi-days trips. The incremental integer values of the three exponents can be easily explained with a three-scale mobility cost∕benefit model for human displacements based on simple geometrical constrains. Essentially, people would divide the space into three major regions (close, medium, and far distances) and would assume that the travel benefits are randomly∕uniformly distributed mostly only within specific urban-like areas. The three displacement distribution zones appear to be characterized by an integer (1, 2, or >3) inverse power exponent because of the specific number (1, 2, or >3) of cost mechanisms (each of which is proportional to the displacement length). The distributions in the first two zones would be associated to Pareto distributions with exponent β = 1 and β = 2 because of simple geometrical statistical considerations due to the a priori assumption that most benefits are searched in the urban area of the city of residence or in the urban area of specific nearby cities. We also show, by using independent records of

  14. Multi-scale analysis of collective behavior in 2D self-propelled particle models of swarms: An Advection-Diffusion with Memory Approach

    NASA Astrophysics Data System (ADS)

    Raghib, Michael; Levin, Simon; Kevrekidis, Ioannis

    2010-05-01

    Self-propelled particle models (SPP's) are a class of agent-based simulations that have been successfully used to explore questions related to various flavors of collective motion, including flocking, swarming, and milling. These models typically consist of particle configurations, where each particle moves with constant speed, but changes its orientation in response to local averages of the positions and orientations of its neighbors found within some interaction region. These local averages are based on `social interactions', which include avoidance of collisions, attraction, and polarization, that are designed to generate configurations that move as a single object. Errors made by the individuals in the estimates of the state of the local configuration are modeled as a random rotation of the updated orientation resulting from the social rules. More recently, SPP's have been introduced in the context of collective decision-making, where the main innovation consists of dividing the population into naïve and `informed' individuals. Whereas naïve individuals follow the classical collective motion rules, members of the informed sub-population update their orientations according to a weighted average of the social rules and a fixed `preferred' direction, shared by all the informed individuals. Collective decision-making is then understood in terms of the ability of the informed sub-population to steer the whole group along the preferred direction. Summary statistics of collective decision-making are defined in terms of the stochastic properties of the random walk followed by the centroid of the configuration as the particles move about, in particular the scaling behavior of the mean squared displacement (msd). For the region of parameters where the group remains coherent , we note that there are two characteristic time scales, first there is an anomalous transient shared by both purely naïve and informed configurations, i.e. the scaling exponent lies between 1 and

  15. Comment on "An improved gray Lattice Boltzmann model for simulating fluid flow in multi-scale porous media": Intrinsic links between LBE Brinkman schemes

    NASA Astrophysics Data System (ADS)

    Ginzburg, Irina

    2016-02-01

    In this Comment on the recent work (Zhu and Ma, 2013) [11] by Zhu and Ma (ZM) we first show that all three local gray Lattice Boltzmann (GLB) schemes in the form (Zhu and Ma, 2013) [11]: GS (Chen and Zhu, 2008; Gao and Sharma, 1994) [1,4], WBS (Walsh et al., 2009) [12] and ZM, fail to get constant Darcy's velocity in series of porous blocks. This inconsistency is because of their incorrect definition of the macroscopic velocity in the presence of the heterogeneous momentum exchange, while the original WBS model (Walsh et al., 2009) [12] does this properly. We improve the GS and ZM schemes for this and other related deficiencies. Second, we show that the "discontinuous velocity" they recover on the stratified interfaces with their WBS scheme is inherent, in different degrees, to all LBE Brinkman schemes, including ZM scheme. None of them guarantees the stress and the velocity continuity by their implicit interface conditions, even in the frame of the two-relaxation-times (TRT) collision operator where these two properties are assured in stratified Stokes flow, Ginzburg (2007) [5]. Third, the GLB schemes are presented in work (Zhu and Ma, 2013) [11] as the alternative ones to direct, Brinkman-force based (BF) schemes (Freed, 1998; Nie and Martys, 2007) [3,8]. Yet, we show that the BF-TRT scheme (Ginzburg, 2008) [6] gets the solutions of any of the improved GLB schemes for specific, viscosity-dependent choice of its one or two local relaxation rates. This provides the principal difference between the GLB and BF: while the BF may respect the linearity of the Stokes-Brinkman equation rigorously, the GLB-TRT cannot, unless it reduces to the BF via the inverse transform of the relaxation rates. Furthermore, we show that, in limited parameter space, "gray" schemes may run one another. From the practical point of view, permeability values obtained with the GLB are viscosity-dependent, unlike with the BF. Finally, the GLB shares with the BF a so-called anisotropy (Ginzburg

  16. Multi-scale measurements and modeling of denitrification in streams with varying flow and nitrate concentration in the upper Mississippi River basin, USA

    USGS Publications Warehouse

    Bohlke, Johnkarl F.; Antweiler, Ronald C.; Harvey, Judson W.; Smith, Richard L.; Voytek, Mary A.; Laursen, A.; Smith, L.K.

    2009-01-01

    in NO3 - concentration. Hypothetical models based on our results illustrate: (1) U denit was inversely related to denitrification rate constant (k1denit, in day-1) and vertical transfer velocity (v f,denit, in m day-1) at seasonal and possibly event time scales; (2) although k1denit was relatively large at low flow (low NO3 -), its impact on annual loads was relatively small because higher concentrations and loads at high flow were not fully compensated by increases in U denit; and (3) although NO3 - assimilation and denitrification were linked through production of organic reactants, rates of NO3 - loss by these processes may have been partially decoupled by changes in flow and sediment transport. Whereas k1denit and v f,denit are linked implicitly with stream depth, NO3 - concentration, and(or) NO3 - load, estimates of U denit may be related more directly to field factors (including NO3 - concentration) affecting denitrification rates in benthic sediments. Regional regressions and simulations of benthic denitrification in stream networks might be improved by including a non-linear relation between U denit and stream NO3 - concentration and accounting for temporal variation.

  17. Multi-scale measurements and modeling of denitrification in streams with varying flow and nitrate concentration in the upper Mississippi River basin, USA

    USGS Publications Warehouse

    Böhlke, J.K.; Antweiler, R.C.; Harvey, J.W.; Laursen, A.E.; Smith, L.K.; Smith, R.L.; Voytek, M.A.

    2009-01-01

    - concentration. Hypothetical models based on our results illustrate: (1) U denit was inversely related to denitrification rate constant (k1denit, in day-1) and vertical transfer velocity (vf,denit, in m day-1) at seasonal and possibly event time scales; (2) although k1denit was relatively large at low flow (low NO3-), its impact on annual loads was relatively small because higher concentrations and loads at high flow were not fully compensated by increases in Udenit; and (3) although NO3- assimilation and denitrification were linked through production of organic reactants, rates of NO3- loss by these processes may have been partially decoupled by changes in flow and sediment transport. Whereas k1denit and vf,denit are linked implicitly with stream depth, NO3- concentration, and(or) NO3- load, estimates of Udenit may be related more directly to field factors (including NO3- concentration) affecting denitrification rates in benthic sediments. Regional regressions and simulations of benthic denitrification in stream networks might be improved by including a non-linear relation between Udenit and stream NO3- concentration and accounting for temporal variation. ?? 2009 The Author(s).

  18. Local variance for multi-scale analysis in geomorphome